This sounds like a bug, where that bug would be I am not sure. I had a guess where it might be in how taking a reference to the hash value might interact with Tie::IxHash, but I could not demonstrate any misbehaviour. (I was playing around with tying a hash to Tie::IxHash, building up the hash, taking a reference to a hash value and then manipulating that value both through the reference and through the hash.)

Can you produce a minimal code example that shows the problem with directions for how to run it and how it misbehaves? If you do that, then I can try to run it and see if it misbehaves for me. If it works for one person and not for another, it may be that the bug is fixed and all that you have to do is upgrade.