I have DOSbox installed on my Ubuntu linux box, and while it works I am having a problem with the conf file. I set it up the way I want it, copy it to the appropriate directory and it works but after a couple of runs of dosbox it for whatever reason stops using the conf file.
Any suggestions?
Just to get the painfully obvious out of the way, you are running the dosbox from the directory with the dosbox.conf and the app every time?
Because dosbox uses the dosbox.conf from whatever directory it is ran from and if it finds none will default to ~/.dosboxrc. So if you run the dosbox from the right directory a few times then forget to run it from the correct directory after that it will definitely not find it. Or from how you say you alter the dosbox.conf if you run it from where you altered the dosbox.conf, it will only find that dosbox.conf and not the dosbox.conf in the app's directory.
If this is not the case I apologize but I have found it best to check out the obvious first.
The only suggestion I have otherwise is to make a copy of the dosbox.conf and then run the game a few times. After it stops working try comparing them and see if there are any differences.