I am using 3.7e
I just started a fresh game of Wario Land 4. I had no existing Save files what so ever.
I played the entry passage level and the first boss. (I also did a RTS once I finsihed this). I turned the DS off and back on to check if my progress had been saved. After starting again it had nothing saved. I had to start again. The RTS worked.
The system automatically has created a .is0 and .sav file.
I deleted all saves created and started again I completed entry passage level and the 1st level of emerald. I went back to the main massage and then turned off and on. Loaded and my save game was there with first emerald level completed. I then reset again and started a new game from 2nd save space. I comlpeted the first ruby level walked to the main hall and then restarted and my save game was there.
Super Mario Advance - played first level pressed START and went save and quite after second level started. restarted DS and Game was successfully loaded.
Super Mario Advance - played first level, after second level started I turned off DS. Loaded SMA again and it had not saved (You have to press Start, Save and Quite or Start Save and Continue)
Yoshi's Univerrsal Gravitation - Auto Saves after level completes. After restarting save was there fine
Super Mario Advance 4 - Finished first Level - Went Save and Quite and then turned DS off / on loaded game and it had saved successfully.
All files created are is0 and sav.
I hope thsi information helps you with your two games mentioned.
I also have a previous backup of Castlevania and it was .0 and .is0 and I renamed the .0 to .sav and it loaded my save game fine and I was able to continue to save and reload.
I would also appreciate it if you could upload the save files somewhere so I could test - that would be really neat