When using a KDE Plasma desktop, KWallet is the preferred backend. Its presence is detected by calling the DBus API with a short timeout. This timeout can easily be reached when KWallet is slow to respond (for example, when it has been paged out, and there is a lot of other disk activity). QtKeychain now falls back to Secret Service, which succeeds because KWallet does implement that API as well, but it stores the secrets in a different location so the previous ones now appear lost.
This would probably be fixed by #221 (well, after causing all secrets to be lost once), or #75 could offer the user a workaround.