Try to start the games without the special controller and plug them in when you are in the main screen of the game.
If this won't help maybe the modchip is affecting the usb ports.
For deactiving the chip or unsoldering the power for the chip you should look at the manual or soldering diagrams of the chip.
PS2 SCPH-70004 V12 PAL + HDCOMBO + 160 GB Samsung HDD + OPL 0.9.1
PS2 SCPH-70004a V13 PAL Satin Silver
2 x Official Sony 8mb card +FMCB 1.8c + uLE 4.42b
Datel Max Memory 32mb card +FMCB 1.8b + uLE 4.42
Memor32 + Memento FW 1.2e