Emergency tax code and overpaying on tax

I have a problem wrt that I am paying more tax than I should.

I feel that the reason being that during the summer I decided to take on some freelance locum work. I registered with IR as being self employed. My earnings for that period were £480, however I had a lot of traveling expenses and had to buy indemnity cover as well. I got exempt from class 4 NI contributions as the amount that I earned was so little. The self employed period lasted 2.5 weeks.

When I started my permanant job in Aug. I was put on an emergency tax code. 503L W1/M1 As a result I am being overtaxed. My colleagues who are on exactly the same salary receive about £460 a month more that I do.

I spoke to the IR and they said that I would have to sort it out in April. This seems a little harsh, and also the government are known for c*ck ups and delaying in paying out... eg CSA

Does anyone know how to best proceed?

The other question I have is as part of my work I need to be registered with the GDC, BDA, and have indemnity

GDC £660 BDA £111 Indemnity £250

I was told by an accountant that everyone has a threshold of £5000 that they do not pay tax on, and I could write to my local tax office with proof of the above and they would increase the threshold.

A code of 503L means that you have been allocated the basic annual personal allowance of 5035p.a. - the same as most other people - and will not pay any tax on earnings of less than this.

AIUI, the W1/M1 bit simply means that every payday is treated as though it were the first one in the tax year, and you will be given an appropriate proportion of the annual allowance to be offset against that week or month's pay. All this means is that anything which happened prior to the start of this employment is disregarded - so you won't automatically receive a refund for any overpaid tax in previous employments (or self employment). But your take-home pay for each pay period should be exactly the same as that of any of your colleagues whose gross salary is the same as yours and who have a 'normal' basic tax code.

If it isn't, there must be some other explanation - it ain't because of your tax code!