I just restarted your excellent mod after some months off. I immediately noticed that pushing ALT didn’t slow me down – he always walks VERY fast. Pushing SHIFT increases the speed even further. I don’t recall this problem from the last time I played. I found some fixes involving Autoexec.cfg and Config.cfg but they didn’t seem to work for me. I also found a note from the devs in the Steam forums that a fix was in process, but that was a long time ago. I’m using the Steam version and auto-update is turned on. Is there something I’m missing?
There is a check box in the options for turning off always run. Try that and see if it fixes your problem.