Just so we are on the same page: when you drag a muxed file to the Timeline, you can set which VT you place it on. However, there is a limitation on where its Audio will go. This is dependent on how your Sequence is set up and the channels per each specific Track. What happens if your Sequence is set up with, say 4 stereo Audio Tracks (AT's), and your muxed Audio is mono, PrPro will create a mono AT for you. If you already have one, it will try to place the Audio Clip there. Now, even though they may be separated from each other by some other AT's and even VT's (Video Tracks), they are still linked. As such, when you Razor the Video Clip, its linked Audio Clip should be cut too. If not, something is wrong. Did you Unlink the Audio and Video Clips?
As a workaround, you can Lock all other Tracks (Video and Audio), except for your one VT and its linked AT. Move the CTI (Current Time Indicator) to where you wish to Razor, and hit Ctrl-k. This should cut both of your unlocked Tracks' material.
If this still does not work, Alt-click you Video Clip and use the Razor. Do not do anything else yet. Alt-click you Audio Clip and use the Razor. The Razor will want to "snap" to the CTI, so you should be able to hit the same exact spot on each.
Make sure you have both the video and audio tracks you want to razor selected.
The same thing was happening to me. I'm editing AVCHD files with 5.1 audio, so the audio was on track 5, and the video was on track 1. The video and audio were linked, but there were empty tracks between them. I deleted the empty audio tracks, but that still didn't work.
But, as soon as I selected both tracks (by clicking near "Video 1" and "Audio 1" at the left of the timeline panel so both the tracks are highlighted), using Ctrl+k to razor all worked just fine (split both the video and audio).
Hope this helps. Good luck!