Has anyone had experience with script inconsistencies?

I've just had the experience here that a script being executed by the engine is not the same version as the last one that was uploaded. The way I found out was through reactive debugging. That shows you the real script being executed. It was different from the script I opened from the repository. The differences were minor: just some changes in Time of Day steps.

The way to solve this is re-uploading the correct version of the script (the one from the repository).

I've also had the occasion where a script upload was not executed on both sides of the HA system. Although the upload was "successful", the new script was missing on the slave server. We only noticed after a fail-over.

Anyone else with these kinds of issues when it comes to uploading scripts?
Any remedies?

Regards,
Koen