Just some updates. After 3 bad 322s, 1 bad 160, a new adapter and a new burner, I have a (mostly) working Pulstar. At this point, I don't really know what happened to the double bank burning issue. I attempted to eliminate everything by getting new equipment one by one. In the end, all I know is:
1. original burner is not damaged (now I have 2 TL866

)
2. original adapter probably was not damaged (now it is damaged after desoldering headers with very tight fit)
3. original ZIF socket might be iffy coupled with #4 below
4. I used a new lead-free(SN100C) solder, this became a MAJOR pain in the butt as it would NOT clean off the legs to get good contact with burner
5. this adapter will always show OE pin 21 to be not detected. I used a new burner, new adapter, new ZIF, new 322, it showed OE pin not detected, but burns fine.
What I think might have happened is the lead-free solder might have left some legs with bad contacts to the burner, it might have been ok during initial check but during programming it's intermittent which caused the chip to get damaged or routed signals to 2 banks, and this caused it to program 2 banks at a time. What confused me the most was because multiple 322s and 160 were showing the same issue, so it appears it's a burner/adapter issue. Although reads are perfectly fine from masked rom as a test. Eventually with the new burner and adapter and ZIF socket, multiple cleaning of EPROM legs, I found some EPROMs were damaged while most survived.
Lessons learned are, clean the legs, double check (322 vs others) programming switch, double check pin contact before programming, double check burned eprom.
As for the game, I saw some slow down during game play with lots of sprites and some weird graphical issue during the slow down, not sure if this is normal as I've never played Pulstar before. I will play the MAME version to confirm. The graphical issue looks like a big chunk of the screen is skewed/shifted. Like someone sliced the screen at 45 degree, slide that chunk a bit so now you have some part of the screen that is shifted. It only happened during the slow down, so it could be just caused by the slow down? Background music is also strange as if it's not playing the correct track almost, but again, I've never played Pulstar before, so I don't know if that's normal, to be confirmed. It's possible that my V rom interleaving is wrong. I split V1 file into V1 V3 EPROM and V2 file into V2 V4 EPROM. Worst case I swap V2 and V3.