Hmmm, that "N/A" for the "Current FW version on flash:" is a bit worrying.
Next thought, is that command you're quoting correct? It kind of looks like you've doubled up the options or the command or something?
If you do go ahead and burn the card with -skip_is, would you be ok to report back if it works? I think I used to do something similar with the old Infinihost III cards I bought on eBay several years ago, but I'm not sure. It's been a long time. That it's not detecting the current firmware version definitely worries me. I think it should be detecting that ok.
Have you made a backup of the firmware and config options already on the card? (mstflint can do this too)
I always do, just in case. Haven't needed to revert to original firmware yet on any of the IB cards I've bought from eBay, but if I do at least I'll be prepared (I hope).
I just had a similar experience with the current fw version on flash displaying n/a and a DIFF DETECTED error. Used skip_is and so far so good.
C:\mstflint_x64_2_7_2>mstflint -d mt25204_pci_cr0 -i fw-25204-1_2_0-MHGS18-XSC_A4.bin -skip_is burn
Current FW version on flash: N/A
New FW version: 1.2.0
Read and verify Invariant Sector - DIFF DETECTED
Invariant sector mismatch. Address 0x4 in image: 0x07400240, while on flash: 0
The invariant sector can not be burnt in a failsafe manner.
You can continue the FW update without burning the invariant sector.
See FW release notes for details on invariant sector updates.
Do you want to continue ? (y/n) [n] : y
Read and verify PPS/SPS on flash - OK
Burning first FW image without signatures - OK
Restoring first signature - OK
Cool, that's good news.