Bad Plextor 241040A firmware update

[soulripper]

Hello, I'd like to ask you how I can determine if my Plextor burner has been good or bad flashed. Because I've updated my firmware to v1.03 (self-extract install), but the sfx had been infected by a virus and I saw it only after having flashed. I can see v1.03 in the bios and had a success message after having flashed the burner. But today, I've noticed a decrease in reading performances, especially CDRs' burned with the Plex itself. I've used Imations 80mn 16x CDs' (burned at 16x, nero 5.5.6.9 with burnproof enabled, source: 7200rpm maxtor, nothing in background, defragmented hard drive).
Bad flashing or bad CDRs' ?
I know there is a DOS patcher, but don't know how to use it.
Thanx for you answers.

[soulripper]

Thanks for your answer
This time, I'd like to flash in dos mode. Can you help me with the command line ?
I think it's something like that : flasher.exe /2 firmware.bin, but I'm not sure. My burner is MASTER on SECOND IDE.
Do you know how to do ?
Thanx