I've gone through a lot of research regarding the alarm for my car (1.9 1998), and I can tell you that the alarm I have is just a rebadged Gemel GR48. The key fobs and instructions are the same.
Now, there's a passive self-arming feature (which sounds like you described), but that should be an install time configuration. Having said that, a cursory search in the intertubes returned at least one other owner having this thing happen to him after the battery on his fob died...
Non-BMW or BMW branded
key fobs that should work look like this:
The non-BMW branded user manual from Gemel I have is in PDF format, and I don't think I can attach here. So, a couple of pictures of the manual to follow:
Basically, I think you will have to contact a BMW dealer, or someone familiar with the Gemel alarms to reprogram it… The option provided to disable the function temporarily is: