I've been using TeXstudio for a couple of days and the problem happened twice. Maybe it happened upon opening TeXstudio, maybe upon closing documents and opening a different one. Some build command stops working, TeXstudio saying it cannot execute the command (first time it happened to Compile & View and maybe Compile, second time to View). Then in options in Build tab I see default commands with standard names, but in the drop-down lists I see txs:// commands. When I select the appropriate txs:// command, the command starts working. Then (probably after a restart of TeXstudio) when I open options the commands in drop-down menus have their normal names again.
I'm using a portable version of TeXstudio (not from Program Files, UAC is disabled).
Which version of TXS? Are you switching between the simplified and the advanced configuration?
I've updated since then. It must have been the up-to-date release version. I don't remember switching between configurations. Do you mean "Show Advanced Options" in Options?
The bug didn't happen again since then.
Last edit: GrayFace 2017-04-16
There's been a bug that could cause to overwrite the command definitions in one of the more recent versions. This had been fixed in the current release.
I assume, you've encountered this. Please report back if it happens again.