Yes, well, as I said, it would be better if mIRC had a switch to make both cases possible, but..
The automatic timer naming functionality in mIRC is a convenience for the simple case (a one-off timer to message someone or something). You should not rely on this functionality for scripts, especially those that need to access $timer(NAME) --for this very reason.
Similarly, you should consider numeric timer names as "reserved" in mIRC for the above simple case "auto increment" timer names. As such, you should not try to name any timers in this "namespace", since it is reserved for said timers. Of course, this is not a rule, just something of a convention. The easy fix here is to just name your timer something that is not numeric, as was mentioned, and stay away from stepping on mIRC's toes.