You might want to use the new file handling functions (/help /fopen), as they speed up writing/reading a lot. Then maybe it could even get passed through this issue, I'm not sure though.
BTW, if you're using $read to read all the lines from that file, I suggest using /loadbuf instead.
Speaking of /loadbuf, if your bots were ran on the same mIRC session, you could also "cache" your file in an window, read and write info from/to it, then /savebuf on disconnect. Doing so, you'd access your file less times.