If there are other people with this problem, this is what I did: open synaptic, mark “checkgmail” for complete removal. Then go to http://checkgmail.sourceforge.net/#download and choose the tarball package. After downloading, browse to the folder and extract the tarball (you can also use the terminal of course). After extracting, go to the newly created checkgmail folder in the terminal and type the following:
sudo chmod +x checkgmail
sudo ./checkgmail
This way you run the file “checkgmail”, and the checkgmail settings window opens.
Unfortunately, the link in my application menu was gone, and checkgmail wasn’t in the startup list anymore. To fix this, I went to preferences -> sessions and clicked “ADD”. This opens a new window, type “checkgmail” for the name and for the command you can click browse. This way you can navigate in nautilus to the folder where you extracted the tarball, and select the checkgmail file. Do the same thing in preferences -> Main menu to get your icon in the applications menu back.