I'm having the same issue on an early 2008 Mac Pro (8-core Xeon, 12GB, mirrored 3TB, with separate 1TB and 2TB boot drives (Mountain Lion server and client, respectively). Now have Mavericks installed on a new Kingston 120GB SSD, which is where the problem shows up.
At first I thought it was a hardware conflict with the new SSD drive I'd installed (mounted directly on a PCI-e SATA 3 card...very elegant!!).
I installed Mavericks on the new drive, restored my apps and user folder to it, rebooted to it and all worked....until both my Logitech diNovo keyboard and Apple trackpad will stop working for 30 seconds or so at a shot. This happens every couple of minutes, so it makes the installation near-unusable.
Reboot to the old Mountain Lion installation on the other hard drive, and no problems whatsoever, yet the new SSD drive still mounts and is usable with no issues.
The *interesting* thing is that if I launch Call of Duty 4 (or presumably other games...haven't tried as I'm not a big gamer) while booted from the Mavericks drive, both the bluetooth keyboard and trackpad work flawlessly. It's as if the problem is with Apple's BT driver and CoD4 is somehow bypassing it? I played CoD4 yesterday for over an hour with zero problems, but both before *and* after that, the same BT keyboard and trackpad kept dropping out as if they'd lost connection. I plugged in an old USB keyboard and when the BT one stops working, the USB one still does, so the system isn't completely hung...just lost BT.
Really odd....
Anyone have any ideas?
Thanks,
Craig