Ari,
It's very strange that nobody replied to you yet...
I think new update should be rolled out soon, not sure if it will solve any of your issues.

As far as I can tell you have two main issues:

1) Auto renaming mixer track whe you place content.

2) inconsistent/faulty results when exporting audio at different frequencies.

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#1 I think is sort of normal. What underlying content you had with Hi-q Instrument. Was it something chosen, like Real Track chart, Super track or such or you notated it yourself? It might have just defaulted to piano, changing your other track... I wonder if you freeze tracks except for the one you are working on, will it change the frozen track names? This I feel is more of a workflow item, not a bug.

#2. I believe it is fixed in a patch that is being tested now. Hopefully they will release it soon. Sometimes Andrew lets users test patch before official release. If it's somewhat urgent, perhaps you should ask them.