The problem is that PS2 Save Builder supports loading .psu saves but does not support saving as .psu. This was because Vector, who wrote PS2 Save Builder, was unable to test this to his satisfaction (my EMS Memory Adapter died) and so support for saving in this format was removed.
This wasn’t an issue at the time as very few people in the west had this product, but with it now being the format of choice for users of uLaunchElf more and more people are missing the abilty to convert their saves over to .psu
Over at PS2-Scene ffgriever has released PS2 Save Converter, a handy tool that converts between .xps (Xport2 format) and .psu (EMS Memory Adapter format).
When used in conjuction with PS2 Save Builder, this allows conversion between all the major formats and even the creation of new save files in .psu format (save as .xps in PS2 Save Builder and use PS2 Save Converter to convert it to .psu)