For any app that is included as part of the rom, updates from the market generally won’t install. This is because they are in system/app, and are designated as read only (unless, like some roms, there is a mechanism that allows system apps to be moved to data to allow for updates). If you really want the updated app, and don’t want to wait for an update to the rom, you can accomplish it in one of three ways.
the easiest way is thru root explorer. go into system/app, and then click the "mount r/w" button (to change the system files from read only to read/write). then find the app, long press on it, and then hit "delete". then push the "mount ro" button to change back to read only, exit out of root explorer and then reboot (this is important to get the change in system apps to "take.") when you boot back up, you should be able to install the app from the mkt, with the update.
the second avenue is thru Terminal Emulator. type in:
su
sysrw
rm /system/app/[name of app].apk
sysro
reboot
again, it's necessary to actually type in "reboot" and enter, to get the change to take.
finally, you can go into the rom zip file, manually delete/remove the app, and then reflash the newly configured rom zip file w/o the system app. then you should be able to dl the updated app from the market.