When you make a psx eboot you have to choose an SLUS code. It will be SLUS (or SCPS, SLPS, etc etc) followed by a series of numbers, this is basically a serial number or part number for a psx game. Each one has one and the same game may have different ones based on region.
Here's a website of some example ones:http://www.dcemu.co.uk/vbulletin/threads/62637-SLUS-Code-adjustments-for-POPstationhttp://www.digitpress.com/forum/archive ... 45473.html
The issue is that with psx games the psp makes a save directory based on the SLUS code. So if your new eboot wasn't made with the same SLUS code as your old one was, then the savegames for each will be in different directories. You'll see in your psp's SAVEDATA directory a bunch of directories that are just called SLUSXXXXX (the X's represent numbers) and these are the saves for each psx game.
So you can go into the save directory for your old eboot and move it over to the new one if you can figure out which is which. Here's a good list of what SLUS code is for a certain game. Hope that can help you out. http://gamerspress.com/mediawiki/?title ... ility_List