Query on more than one entry clearance for ILR work permit

[man18]

:?:
My employer got first Work Permit on 19/01/2003 and I got the Visa stamped on 27/01/2003 in my country. This was valid until 27/01/2004. I arrived in the UK on 03/02/2003.

I left UK on 04/12/2004 and stayed in my country for around 50 days. During this time it was not sure, whether I can come back by 27/01/2004. My employer got another work permit on 10/01/2004 and I got it stamped in my country on my passport on 20/01/2004. Finally I arrived back on 24/01/2004. On that day I had two valid visas that is one was expiring and another one was new. After that I have always taken FLR in the UK itself.

I have all P60s till date with me. Above 50 days are without pay and I have not got salary slip only for these two months. My salary was paid again only from 24/01/2004 onwards.

I have availed paid holidays all the time in five years two weeks in easter and three weeks during October. My total days outside the UK are 202. I have all salary slips for rest 152 days indicating I have been paid in UK.

I have a specific query with the absence. Has the clock been reset after the second entry.Home office says that it is discretion of case worker!!!