I'm having the exact same issue pop up. I'm using a J-pac board and connect to a 15khz arcade monitor. I thought the whole system was working perfectly, as I had run several tests on video, controls, and sound before I commited to switching my DOS based (advance mame/menu) to Maximus Arcade. Once I was confident everything was working perfectly, I spent hours doing the conversion, setting up the emulators, and copying all of my roms.
It wasn't until I had everything done, then I noticed this issue pop up. I tried to track it down by unplugging the USB mouse and keyboard, and just running with the PS/2 keyboard connected through the J-pac. I also use a USB-PS/2 Cable to connect my PC to the J-pac. The issue seems to happen intermittently so I can't track the bug.
It's the same issue as described by another user in this thread: I can use my arcade controls and keyboard just fine in any other aspect of windows and when an Emulator is running, but the controls and key presses aren't recognized within the Maximus Arcade UI. I can still use a Gamepad to move around the menus when the bug occurs. As I mentioned, this seems to happen intermittently, and can be resolved by rebooting a few times. It's working at the moment, so I'm afraid to shut down the system

On a side note, I'm VERY VERY impressed with Maximus Arcade. You've done an absolutely amazing job Mameseer! I was having a few audio issues within my DOS based setup, and setting up any other emulator other than MAME was a pain in the ass at best. Your program has made it SO freakin easy! I've set up 5 or 6 different ones so far with full Video previews of each ROM. I haven't bought a REG code yet, but I plan on it very soon.
I hope this issue gets resolved soon in an upcoming release, otherwise it's a fantastic piece of software! Keep up the great work Mameseer!
Matt