First, many thanks to @firstone for this plugin. eISYIR has the honor of being in slot #1 on my eisy.
I have the same setup as you, a Harmony Elite remote and hub, with one of the ISY994 IR command sets installed and had the same issue.
After doing some research on the FLIRC forums, I found this is a common issue where remotes will alternate two (or more) different codes for the same button. For example, first button press sends code X, second press send code Y, and then repeats. This is apparently the case with the Harmony ISY994 command set used.
The fix for me was to record both codes for each letter (key) on the FLIRC keyboard device by doing two record operations using the same FLIRC key and the same remote button, thereby sending both codes to FLIRC. (FLIRC can hold multiple codes for each key.) I have had zero issues with eISYIR since.
I did this set up early on, before anyone had posted the FLIRC command set files that can just be uploaded. Others have had success with that method.
Hope this helps.
-George