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I am going to apply for my ILR within next few weeks. I came to UK Oct 2004 on working holiday maker visa and then converted into work permit visa. My initial work permit was granted Jan 2006, I went for entry clearence to my native country and it was granted Feb 2006 and I entered UK Mar 2006. This 1 page work permit mentioned "in country decision", will this be a problem?

I went back to my native country Oct 2006-Nov 2006 for a month for marriage, it was a paid leave and I ordered bank statement to prove that(even though I am not sure if I will receive it by the time I apply for ILR) and I also got a payslip for Nov 2006 but unfortunately Oct 2006 payslip is missing.

I went back to my native country Oct 2007 for 20 days and I got payslip and bank statement to prove that it was paid holiday.

I went to Germany 20th Oct 2008- 5 Nov 2008 to attend a conference which was a business visit paid by my university employer, however 8 of those days I was in holiday as well. I dont have a letter to prove that it was a business visit though. However I can prove from bank statements that it was paid.

I went to USA Nov 2009 for a conference for 7 days paid by my university employer and I got a letter to prove that it was a business visit.

Now I am with a different employer for whom I was in Europe in 3 times 11 days in total and I got letter to prove that they are all business visits.

I know that 180 days in total is allowed. My question is do they include paid or business visit absences? I have got zero unpaid absence, around 75 days paid leaves and around 25 days business visits. Is that ok?

All leaves paid or unpaid should be counted, no single absence be >90 days. For business related leaves, you need a letter from your employer explaining that these were official trips, they may then be excluded from the 180 days count.
Hope this helps
Best regards