You should talk to the IRS. You still might collect unemployment. Go ahead and file…you still have pay stubs from previous pay dates, correct?
Wiki on misclassification of employees and independent contractors.
IRS website: Independent Contractor (Self-Employed) or Employee?
By paying you the IC rate of $5600, they are trying to avoid paying their share (and your share) of Social Security and Medicare of $428.40 each. (7.65% each, 15.3% total). Also, they maybe avoiding paying their share (and maybe your share) of unemployment, disability, etc. at either or both Fed and State levels. When you call, the IRS may perk up when you inform them that you were classified as an employee for most of your work history with the company except for the final payment. It sounds pretty cut and dry to me…and this is coming from me, an employer. Boneheaded move if you ask me.