By default, GBA ExpLoader keeps saves in the \GBA_SAVE\ folder, not the \GBA\Save\ folder like the 3in1 ExpPack Tool. Either move the files, or specify the folder you want to use in the GBA_ExpLoader.ini file.
You may also need to rename the save files. Rudolph thankfully did away with the horrible save naming scheme he used in the 3in1 ExpPack Tool, so now the saves are given the same filename as the rom instead of using the internal name and game code.
Also, you can disable the annoying multisave feature by uncommenting the appropriate line in the GBA_ExpLoader.ini file (just remove the # from the beginning of the line).