The Logic Pro 9.1 update includes support for 64-bit native mode, compatibility with 64-bit Audio Unit plug-ins, and support for file names over 32 characters long. According to the update notes, samples are now mapped correctly when using the "Contiguous Zones" opetion in the EXS editor. The full release notes are available for viewing here.
MainStage 2.1 also includes 64-bit native mode and compatibility with the 64-bit Audio Unit plug-ins. Other fixes and improvements include better compatibility with MainStage 1.x documents, improved recording when using the Loopback plug-in, and multiple playback plug-ins in the same group now sync reliably. Full release notes are available here.
Enabling 64-bit native mode for both applications requires Mac OS X 10.6.2 or later.
[A tip of the studio professional hat to TUAW reader samw for letting us know about the update]