I use also Protel 99SE and it seems working.
But I build projects always in this way, that a project directory was created and all files stored separate inside this.
This option was named "Windows File System".
Especially if you use some versions control software it must only update files, which are really changed, and not a huge single file.

I never used the Auto-Router, but I have seen a result of it. It looks really terrible, far from any human working.
Maybe, this men was not an expert and the Auto-Router need a lot of guidance (define rules) to get acceptable results.


Peter