There are two different [email protected]
programs. One is the Graphical version which shows the protein working on the screen and is seen in full screen. The other is the Console version that runs in MS Dos and is text only. From the way you discribe it you seem to be using the graphical version.
Quit the program and go to the [email protected]
folder. You will see two icons there that Ploaf is refering to. One is the Work directory and just looks like a folder. The other is Core 65.exe which could be refered to as the engine. It sounds like the engine is not working properly. Right click on core65 and delete it. Restart the program and it should automatically download a new one and start working. If you still have the same problem repeat the above procedure but this time delete the work directory. On restart it should download a new one and go to work. If you still have problems completely remove the [email protected]
program from your system and reinstall it. Hope this helps.