Maybe you have a stuck key? Either a button or a keyboard button is stuck. Give some details about your setup:
Windows?
What type of keyboard encoder (or keyboard hack)?
If you unplug your CP, does it still take a long time to boot? Is your keyboard attached? If so, unplug both and boot it up. Then plug one in, boot and see what happens? Same problems? If you have a keyboard attached, try unplugging it also and boot up too. Try and narrow it down to one or the other if possible.
Of course, it can be something unrelated to this. Just a shot to see if it's something easy.
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Thanks for the suggestions and sorry for the slow response, only got round to opening up the cab this weekend!
I've got an IPac 2 and running Windows, Mame, MaLa. I did a bit of testing and I think its some sort of stuck button (although doesnt seem pyhsically stuck). I used the Ultimarc ipac config tool to test all the buttons and two dont light up when pressed. One is Quit (Esc) but that seems normal??? The other is P1 Button 1 (standard Ctrl) so I think this is where the culprit is. It was also sticking on and not coming off.
I unplugged all, took off the CP and checked the wiring. It all seemed ok but it seemed like P1B1 was not "clicking" when pressed. I took the microswitch out and put it back in and all seemed good for around 10 mins, I was playing a couple of games when the controls all messed up again.
I'm sure there's a clue in teh fact that if i scroll up or down in teh game list it goes up or down by 11 games, I am pretty sure it's somethign around the left CTRL button (B1) but the physical button doesnt seem like there's a problem with it??
Any more ideas? I appreciate the suggestions!