Employer's late bonus payment might screw up my unemployment benefits!

I was terminated from my job for reduction in workforce. I have applied for unemployment. I am worried that I won't be getting the top amount allowed by unemployment because of something my employer did. Here is my story:I am a grant writer. I am paid an hourly wage plus a bonus determined by the amount of the grant. My written agreement with my employer was that I would be paid my bonus upon receipt of the funds from the grant. In March 2003, we were informed that a grant I wrote was approved and that my organization would received over $100K over the next 12 months. After receiving $50,000 my bonus due was $5,000. I should have recived the $5,000 last summer 2003. My employer is in financial difficulties and did not pay me according to my written contract. When he fired me about a month ago I demanded what was owed me and it was paid to me this month. This is going to screw up my unemployment benefits. The $5,000 was earned in 2003 and would have been in my unemployment base period that is used to figure my benefits. Now, with it being paid in 2004 and during the period that unemployment counts as a "lag period", that $5,000 won't be showing where it should be and will have unemployment calculate my benefits incorrectly, in other words I will be paid less than I should be.
What can I do about this? Will I have to take this to court? I just want to be able to collect all that I am entitled to.