I am not 100% sure that I understand you problem, but let me answer what I think the problem is. It seems as if you are creating a GPIB instrument based on the TNT4882 GPIB ASIC. You are trying to assert the SRQ line on the GPIB. When you program the TNT to assert the SRQ, you are not seeing the SRQ line asserted on the bus.
How are you asserting the SRQ (what registers are your writing)? There are three ways to assert the SRQ line on the TNT.
1) Using 488.1 style
2) Using 488.2 style with STBO IE interrupt
3) Using 488.2 style without the STBO IE interrupt
Information about the three different types are described in the TNT4882 reference manual on page 4-13.