You mean Tekmagic?
When did you send it to GVP? Recently? Afaik they haven't been servicing boards in over a decade...
In any case, you shouldn't have any problem using it with a 6.x-series motherboard and the latest 3.1 ROM. Using an '060 under 2.04/2.1 would be like using a Formula 1 race car on "Ron's Discount Retread Tires". Don't do it, it *will* work under 3.1. How do I know? Because I own one, lol. 
If you suspect ROM issues, try with a new 3.1 chip first. You can get a new one for under $20 USD:
http://amigakit.leamancomputing.com/catalog/product_info.php?cPath=25&products_id=157
I'd try that, and start documenting everything you've tried. I.e., does the A2000 boot normally with no accelerator installed, what exactly happens when you try to boot with the board installed, any battery damage, reseated all the custom chips (on the Amiga and on the GVP board), also it might be an issue of your PSU starting to fail and not putting out enough power. Have you tested that?
This page has some additional info that may help you: http://nishtek.com/Riese/GVPTekmagic68060.html
I am in a VERY DETERMINED mode now and will soon have time once again to get back on this project...
RE: Olds-mike,
I have previously done everything you suggested, 3.1 Roms bought for both boards same time. (*see sub note please) it does boot with 68000 and Derringer 030 installed on 3.1 Rom & OS 3.9.
RE:Saccy-guy
I did install those libs (060) on the HDD boot partition as well, but maybe not the 040 libs?
My apologies, yes - it was over a decade ago, and sorry for the Magictek LOL
was not concentrating on what I originally typed .... I did not proofread when typing...
... so I got ticked off at it and threw it in the closet..., I had bought it to build a souped up Video Toaster box for myself
Reasoning for the 2.04 Rom is to get it to a semi-functioning starting point to diagnose my way forward to full functioning, then apply 3.1 Rom...
1 of the friends machines used to test already had a Tekmagic '040 board properly setup and running, so I was able to power mine up in his box and test-ran mine for a couple hours, so I am not suspecting the accelerator board as much. Maybe more in the motherboard?
2 brand new boards 060 boards were purchased @ the same time, not second hand.
I bought the 2, sold 1 to a client (for all the labor in the contract I did, it actually paid for mine) ;-)
I have even done the accelerator issue checks as part of what Dave Haney has previously posted on the web, except checking the a signal startup (can't remember right now which one *S3/S1 or something like that??) that affects some accelerator boards starting.
If I can find those docs, I will try masking the related suggested pin off and see what happens.
I have of course cleaned the contacts, and FYI, whetting a business card with acetone/ Isopropyl Alcohol and sliding it carefully through the CPU socket 1x will clean the contacts, then the cardboard paper starts to deteriorate... of course clean any debris out it creates..
(a HAM Radio trick to clean CW (Morse) keyer contacts)
Dave Smith did find a solder short issue under the SCSI chip on the board I purchased, but I don't remember if he repaired it or just replaced the board (free - under warranty)...
Thanks
I do appreciate all the assistance here from everybody, -
20 heads are better than 1....
I REALLY want to get this board running, it is driving me crazy...
*FYI:
I am a Component Level Electronics Service Technician, (repair/design/hardware hacker)
I was also the last Support Tech @ PP&S before the fire,
was the RMAUG VP 10+years ago
now a jus a Windows Systems/Network Administrator & Engineer
(just for technical competency reference)
gotta get outta here now,
I have to replace both of my site Network CORES tomorrow night here at my call center... :-(