Ok - I'll try and share some more details with you about what I think is happening, in the hope that some of my questions may make more sense to you. I think we need to check a few things further to narrow this down before there is any certainty on what is happening to your system.
NCrunch itself has a very limited presence inside the IDE when the 'Engine hosting strategy' is set to use a satellite process. Basically it's just a synchroniser that pushes changes through IPC into the satellite process to be handled. The mechanism for this is the same for every type of project or solution, and it's very very lightweight. I guess what I'm trying to say here is that I think it's unlikely this problem is directly being caused by NCrunch's VS integration - though it is still quite possible that the issue is being triggered by NCrunch indirectly.
It's known that NCrunch is able to cause poor performance in the IDE through overconsumption of system resources. There are many mechanisms built into the product to try and prevent this, but it can still happen in the following cases:
1. If NCrunch itself is not configured correctly (for example, 'Max number of processing threads' is set too high or the CPU cores are not assigned correctly)
2. If the IDE is attempting to perform excessive blocking I/O activities on a slow disk, NCrunch can block IDE threads by tying up the I/O system with its background processing. There would need to be something wrong with Visual Studio to cause this (a 3rd party package perhaps), as normally VS doesn't heavily block on I/O on foreground threads.
3. If NCrunch is executing tests that tie up system resources in other ways. For example, you may have tests running against an SQL Server Database. SQL Server runs in a process outside of NCrunch's control, so there is no way for NCrunch to stop the database server from overconsuming resources if the tests are particularly taxing. This basically takes CPU away from the IDE and causes poor performance.
All of the above cases can be identified with close attention to system resource utilisation when the problem presents itself. For example, if there is a background process stealing CPU away from VS, this should be visible with around 100% CPU utilisation. If it's I/O that's the problem, you'll likely see a large disk queue.
Finally, there is one more thing that can cause poor performance in the IDE: Memory traffic. It's worth being aware of this -
http://blog.ncrunch.net/post/Engine-Separation-and-VS2015-Integration.aspx. It's entirely possible that the poor performance you're seeing is being caused by a combination of VS, NCrunch, and other installed packages all competing for the same GC. NCrunch should do very little to impact this when it is satellite hosted, but it's not impossible that in this situation NCrunch is the last straw that broke the camel's back.