I'm a first time builder with a K62 case and a P7P55D-E Pro which I'm trying to get into the case, I'm at the point where I need to screw down the motherboard into the standoffs, but the top and middle line of standoffs are narrowly out of line with motherboard. I can manage to make the bottom line of standoffs match the holes on the motherboard though no luck with the top line. I've figured out that the I/O panel uses up just that much space to cause the motherboard to barely not match up. Thing is these are the only standoffs/holes that match up with the motherboard ones, and I'm at a lost for what to do. Should I just screw in the ones I can? Try forcing them in more? Advice would be appreciated!
Perhaps this will help. Line the nine MB holes up with the nine risers. The MB I/O plugins fit tightly into I/O shield/. The I/O shield and MB must match correctly. I find it easier to plug in the front panel connectores to the MB before screwing it down. If you are using the ASUS EZ connector the front panel connectors are much easier to work with.
The case is compatible with ATX MBs. If you are having trouble installing the MB into the case, ask someone who has done it before to help you.
I suspect that your problem is that the I/O panel is not fully in place.
First, check that the rear i/o panel is securely pushed into the opening of the case. It sometimes takes a bit extra force to get it all in. Work your way around the edges. It all should click in. If this is not done, then your mobo will not line up.
Next, the i/o panel will have some spring like tangs. position the mobo i/o ports so that they go into the i/o panel cleanly. Then push the mobo firmly into the i/o panel, compressing those little tangs a bit. You should be able to put in the screw closest to the i/o panel first. I find it helpful to use a #2 magnetic tip screwdriver for this. I can hold the pressure with one hand and position the screw with the other.
I really doubt that the mount positions are not drilled properly. If they are not, then return the case.