Not sure about your versions and what chip you are using, I may be wrong--but from what I've read you shouldn't need to patch a PS2 CD when using a modchip--unless it has Anti-Mod protection, or is an EA Sports Game. A direct copy with CloneCD or CDRWIN should work fine with conventional GS2/AR2 swaps. I have had no problem with CD based PS2's so far.
A DVD-R copy should go as well, except for some dual swap trickery--Night has a method that has worked flawlessly for him in that arena. DVD to CD-R Rips are generally tricky by nature--like Night said, you have the 640MB barrier, among other things--you have to make sure you have the right rip kit for your region, etc.
If the game is "loading", but not working right, it can sometimes be the quality of media, or the burn method (RAW-DAO, ISO96, Don't correct subchannel, slow burn, etc). If it isn't loading at all--anything goes. In my experience, I have never gotten the pink "non-playstation" screen when swapping a disk. It either loads something, or does nothing and just stays black. You might want to double check your swap method, just in case--or try Nights "code updating" method with the GS2.
In case you want to know any of this, I'm using a no plug for v5 NTSC (US) (
www.modchipinc.com/pages/nosolder.htm for $9.99+$5 S/H) with a GS2 v2.11 (Wal-Mart), Jensen 32X silver 80min (Circuit City), or Maxell 24X Gold 80min/74min CDR Blanks (Office Depot), CloneCD Ver. 2.8.3.1 (1st)/ CDRWIN ver 3.9a (2nd), Mitsubishi/HiVal DVD (BDV12B), and Pacific Digital/Lite-On 12X10X32 CDR/RW (12101-B, with Updated LS3J Firmware) On Win98SE with ASPI Drivers installed with CDRWIN 3.9a. Have Prassi Primo installed with updated Px Engine, waiting for some spare $$ to snag a Pioneer 03/04 DVD-R/RW Drive for DVD's--staying away from Rips for now.
Good Luck!
Raist