Re: protel 99 vs protel 2004
Yes, there are many differences between 99/99SE and AD2004. One of the biggest differences is the query language. It uses logic statements to do global operations and searches.
Many of the hotkeys and basic operations are the same. But many of the things you are used to in 99 are done differently in 2004. For example, board outlines and plane layers are handled much differently. Output is handled differently, global searches are done differently, parameters are handled differently, etc.
There is a big learning curve when switching to the newer version. However, the newer version can do much more than the older version. I suggest you take a look at the @ltium (Pr0tel) site, and get a demo version of the software so you can judge for yourself.