Flying blind on this as I don't have an Ultimate unit.

Is all of this happening with Transponder 1? If not, are you just getting the "not locked" return for channels on the EVEN NUMBER transponders? This is a common problem when the 18v output from the box doesn't get thru to the LNB (or in your case, probably to the switch) to change from the odd transponders to the even transponders.

One common cause of this is cabling, as Larry suggested. Check your connections to make sure they are tight and dry. Also check the connectors themselves - even one tiny filament of the sheathing touching the central conductor might be enough to cause this.

Of course, it COULD be a problem with the box not properly outputting the 18v correctly, in which case you have a bad unit. You should be able to check this with a multimeter -- 13v for odd transponders, 18v for even.