We have just made a change to the directory where save games are stored. If you want to continue to use your 2.5-dev savegames with the latest version from git or the nightly installers, you must copy them manually to the new location. Otherwise the game will be unable to find them. The path depends on your operating system and is written in our FAQ.
Files that end in .savx need to be placed in a new subdirectory called campaign. Files that end in .mpt need to be placed in a new subfolder called "multiplayer" (for multiplayer teams) or "skirmish" (for skirmish teams). If these new directories do not exist, just create them.
For example, on Windows you will find the files in \Documents and Settings\\Application Data\UFOAI\2.5-dev\. You must create the folder "campaign" at \Documents and Settings\\Application Data\UFOAI\2.5-dev\campaign\ and move the save files there.