I'm sure you've checked this, but I assume you do have "handle keys" turned on in the DVRMSToolbox Settings, MC Addin tab?
When you say everything works except for key handling, does it skip commercials automatically, just you can't control the addin while it is running?
Gigabyte GA-P35-DS4, Intel Quad Q6600, 4 GB RAM, ATI HD 2600XT 512MB, Enermax 495P PSU, 2x SATA 500GB, 3x SATA 300GB, LG GSA-4167B, Hauppauge PVR-250, Toshiba 51H83 (51" HDTV), Yamaha RX-V2400 Amp, 5x Energy Speakers, SVS Subwoofer