There isn't a problem. I know for sure that the Pokemon games are supposed to have 512kb saves (courtesy of Chase-san who has constantly pounded on that fact). I believe the savlib is for the type of save file (EEPROM, Flash, and all of those other ones in No$GBA), though I've never actually went and looked it up.
In any case, your save files are fine and there isn't anything strange about them.

 

Watch out.

After writing the file is still 512 kb in the directory information but 1 Mb is actually written. So the 512 kb extra data is now written to "somewhere" outside the space allocated for the file. If you are lucky this 512 kb was not allocated but otherwise it overwrote another file or files. Sooner or later you will get in trouble.

The way it was was okay, 512 kb save file while the program would also create a new 512 kb file. With savelib is also okay if your save file is 1 Mb and the program would also create a new 1 Mb file. This will waste 512 kb but will not lead to problems.

But not good is a 512 kb file while the program would create a new 1 Mb file. In that case during save 1 Mb will be written, 512 kB to the file and 512 kB outside the file. There are technical reasons while even this will work for a while, but sooner or later data or the file system will become corrupt.

 

just run the ysmenu as a .nds file and it will work on the r4sdhc from r4sdhc.com