I have never experienced this problem myself. Some users have.

Smscon uses Dbus to detect a receiving SMS message and compares the message text with the predifine texts (AKA commands). If not the same smscon doesn't do anything else in the background. It's all a fairly basic & simple approach, which should interfere with other installed software I think.

Slight delay for new version release (0.7-1). I will send Saturn tomorrow the new user settings/commands to implement (if he has time to do it).