I know nothing about this equipment and application so before you try all these things I'd wait for someone more familiar with using this application but a few things to try...
- Play the audio, use the foot pedal, but don't type. Does it still happen?
- Play the audio, type anything even if you can't keep up but don't use the foot pedal.
- See if the recorded audio files are in a standard format, if so then try playing them back with another audio application.
- I assume windows - Open Task Manager, Processes tab, sort by CPU column and see if any application is taking CPU time when the stuttering happens.
- Try a new audio driver
- Did the problem start happening on same system after no changes on your part? Is it possible you're infected with Malware? Did this system potentially do a Windows Update and that is the cause? You could try to figure out what updates were installed just prior to the onset of the problem, or restore your system from a backup made just prior to onset of problem. Everyone makes backups on production systems, right?
- If no backup available, put a clean windows installation on a spare HDD or SSD leaving it disconnected from the internet (so doesn't fetch the windows updates), install only drivers and this application, and try that.
- Are these audio files stored locally or streaming off a remote internet or LAN server? If internet can you download them ahead of time to your system to try playback?
- If internet streamed audio, look at your modem logs for intermittent connections or low signal levels.