Desperate for help with identifying problem; computer, drivers, or steppers

Put in a lot of time on this and am completely stumped and wanted to get direction from experienced users on what might be the problem here. [problem is that 45 to 90 minutes into the milling the Y axis gets way off {3 inches on one of the test runs} and I have been using candles instead of metal to dial this in]

Bridgeport Series 1 CNC BOSS 5, AH-HA RC500 (has little switches for microstepping so I set them to half step and in the step config went with 200 steps per rev and 2 in microstepping field) which is a 48 VDC system (directly soldered to the 5 pins on each driver to bypass the DB37 original connector), original steppers [step time 25000 step direction 25000 direction hold 20000 direction setup 20000 (could not find any info on the specs for these original steppers), max speed at 60 IPM, max accel 0.5 IPS^2, latency test is decent for ~1 hour (47000 ns) and then checking on it after 2 hours it gets to around 120000 ns) milling 2 pockets in a 4.5" round bar `1144 steel (pockets are such that the most movement is from the Y axis and the stepper got to around 115 F after 90 min). So this problem would've been catastrophic if I were using metal.

The computer is a dell 9100 pentium D dual core 2.8 ghz, 800 mhz bus speed, 2mc l2 cache, 64 bit, 512 mb ddr2 sdram 533 mhz(2 of 4 slots with 256 each), external video card (not sure what the make model is). I removed the creative labs audio card and disabled internal audio in the BIOS.

I want to identify this problem because if it is not stepper related and I put a servo system on and still have problems, I would lose my gourd.

Any input is greatly appreciated

Yes, i get the rtapi error on startup but no errors during the run. Im using the db25 parallel port. Backlash is 0.0015 or less for each axis.