This has been mya problem for me since my childhood.

"A problem for me" is more natural than "my problem," and "since childhood" doesn’t need "my."
「a problem for me」が自然で、「my childhood」は普通「childhood」で十分です。

Although it has troubled me many times, I haven’t been able to get it overovercome it.

Use present perfect ("has troubled") for continuing situations. Also, "get it over" is incorrect here; "overcome it" is the right phrase.
現在完了形（has troubled）が適切で、「get it over」は誤り。「overcome it」が正しい表現です。

I am too optimistic about makingwhen estimations forng how long it wouldill take me to get to the station or meeting spots, so I ends up getting therearriving at the very last minute.

Use "when estimating" (not "about making estimations"), "it will take me" (future tense), and "I end up arriving" (correct subject-verb agreement). Also, split into two sentences or use "so" to avoid a comma splice.
「when estimating」が自然で、「will take me」が正しい未来形です。「I ends up」は主語と動詞の一致が間違いで、「I end up」が正しいです。文を分けるか「so」を使います。

I am especially cautious about never to be late for any critical meetings or international flights, and f. For these schedules, I plan with sufficient buffer time,—usually three times as long as usual.

"Cautious about never to be late" is awkward; better: "cautious never to be late." Also, split into two sentences for clarity and use "usually" for natural phrasing.
「cautious about never to be late」は不自然で、「cautious never to be late」が正しいです。文章を２つに分け、「usually」を入れると自然です。

In Despite of all these efforts and care,precautions, I still I often arrive at the last minute.

Despite" is better than "In spite of" here for smoothness. "Care" should be "precautions" for meaning. Also, "I still often" sounds better than "still I often."
「Despite」がより自然で、「care」より「precautions」が適切です。「I still often」が正しい語順です。

I am sovery grateful for that home-based work style is allowed in my current jobmy current job allows a home-based work style because there is much less pressure regarding punctuationlity.

Remove "for that," say "allows a home-based work style," and "punctuation" should be "punctuality."
「for that」は不要。「allows a home-based work style」が正しい表現です。「punctuation」ではなく「punctuality（時間厳守）」が意味に合います。

This has been mya problem for me since my childhood.

What you wrote makes sense, but most English natives would say "a problem for me" since it sounds less extreme.

Although it troubled me many timeshas caused me a lot of trouble, I haven’t been able to get it over it.

"Cause (someone) trouble" is more common. "To trouble (someone)" can sometimes carry a connotation of emotional distress instead of only practical consequences. Not sure if that's what you intended.

I am too optimistic about making estimations for how long it would take me to get to the station or meeting spots, and I ends up getting there at the very last minute.

I am especially cautious about never to bebeing late for any critical meetings or international flights, and for these schedules,events I plan with sufficient buffer time, three times as long as usual.

I am so grateful for that home-based work stylthat working from home is allowed in my current job because there is much less pressure regarding punctuationlity.

Work from home/working from home/working remote/WFH are all very common terms these days in a corporate environment.

Punctuation = 句読点, punctuality = 時間厳守

Although it troubled me many times, I haven’t been able to get it over. it.

I am too optimistic about making estimations for how long it would take me to get to the station or meeting spots, I ends up getting there at the very last minute.

I am especially cautious about never to bebeing late for any critical meetings or international flights, and for these schedules, I plan with sufficient buffer time, three times as long as usual.

In spite of all these efforts and care, still, I often arrive at the last minute.

I am so grateful for that a home-based work style is allowed in my current job because there is much less pressure regarding punctuation.

Although it has troubled me many times, I haven’t been able to get it over it.

(1) "it troubled" probably isn't wrong, but I think "it has troubled" sounds more natural.
(2) In this context, "get it over" would mean something else, such as in the sentence "I got the rock over the wall."

I am too optimistic aboutwhen making estimations for how long it would take me to get to the station or meeting spots, and I ends up getting there at the very last minute.

(1) You are optimistic about the duration needed, not the act of making estimations. Hence, it should be "when" and not "about". Alternatively, you can just remove "making estimations": "I am too optimistic about how long it would take me..."
(2) Although "I" is singular and "end" is typically plural, in this case, "end" would actually be singular and the correct form to use. English can be very inconsistent, I know...

I am especially cautious about never to bebeing late for any critical meetings or international flights, and for these schedules, I plan with sufficient buffer time, three times as long as usual.

Alternatively: "I am especially cautious to never be late..."

In spite of all these efforts and care, I still I often arrive at the last minute.

"still I often" is likely fine, but to native ears, "I still often" probably sounds more natural.

I am so grateful for that a home-based work style is allowed in my current job, because there is much less pressure regarding punctuation for timelity.

(1) I'd suggest adding a comma to break up the rather lengthy sentence.
(2) punctuality: the fact or quality of being on time. "Punctuation" refers to symbols such as the period, comma, exclamation mark, etc.
(3) "for time" is redundant, because "punctuality" already pertains to time.

Although it has troubled me many times, I haven’t been able to get it over it.

I am too optimistic about makingin my estimations for how long it wouldill take me to get to the station or meeting spots,. I ends up getting there at the very last minute.

I am especially cautious abouto never to be late for any critical meetings or international flights, and f. For these schedules, I plan with sufficient buffer time, three times as long as usual.

In spite of all these efforts and care, I still I often arrive at the last minute.

I am so grateful for thate home-based work style that is allowed in my current job because there is much less pressure regarding punctuationlity.