Using free IVA accelerates my vessel randomly and causes it to crash due to low periapsis.

Please post log files with bug reports. At the very least I'd need to know what parts were on the vessel (ideally post a craft file).

The only plausible explanation for this is that there's a collider somewhere that is on the wrong layer and interacts with the parts on the ship. But without more information there's nothing I can do. I'll reopen this when you provide more info and the issue is confirmed.