Are you using any mods or anything? In the new pilot format the stats/progress is stored in the campaign savefile and those aren't (shouldn't be at least) used in multiplayer. They shouldn't be accessed at all in multi mode, just in single. If when you switch back to single mode the campaign savefile doesn't get loaded back properly then it could cause the progress to be wrong.
Try this if you don't mind (with at least some progress on your single pilot): start the game, switch to multi mode on the pilot select screen but DON'T go any further, press ESC to exit the game. Go back into the game and it should still be on multi mode, do a multi game or something (to test reading and saving), DO NOT switch back to single mode yet. Exit the game while still in multi mode and then start it back up, switch to single mode, load your single pilot and go on into the game, check if the progress is still there.
Let me know how that works out. Oh and what build are you using, 3.6.5 or a newer build?