I have the exact same issue as you've described it. I've also read other people have this issue. When experiencing it, it isn't *only* Instant Replay that refuses to work. Manually triggered recordings won't save either. They end up as 1kb corrupted files every time regardless of how long I let it record.
In my case, toggling "Record Desktop on/off" seems to fix it. But I can't tell what causes the bug, and short of checking my replay folder to see none of my funny moments have saved, I can't tell when it's happening... so now I'm checking whether or not the software is actually working throughout the day out of paranoia :/
It's been happening for months now and the lack of attention or a fix is making me want to switch to something that actually works consistently. It's persisted through multiple driver updates and windows updates. -_-