There's a known bug with the G29 code that leaves the extruder head offset from the location the firmware thinks it's at by 25mm in the X direction and (in my case at least) 10mm in the Y. I know it's in the Printrbot Rev F firmware for the Simple Metal; it may be in others as well.
You can confirm this by issuing an M114 command after the G29 process is complete and compare the M114 reported location to what G29 says it was at, and by looking at where the head actually is.
I "fix" this by putting a command like "G92 X132.4 Y20; Reset actual position" in my startup GCODE after the G29 line.
Example:
Send: G28 X0 Y0
Recv: ok
Send: M114
Recv: X:0.00Y:152.40Z:0.05E:12.05 Count X: 0.00Y:152.41Z:0.05 (print head is correctly reported as being at 0,152.4)
Recv: ok
Send: G29
Recv: Bed x: 10 y: 142.40 z: -0.10
Recv: Bed x: 10 y: 10 z: -0.21
Recv: Bed x: 142.40 y: 10 z: 0.04 (G29 is reporting that the print head is at 142.4, 10)
Recv: ok
Recv: echo:endstops hit: X:0.00 Z:0.04
Send: M114
Recv: X:117.40Y:10.00Z:0.05E:12.05 Count X: 117.40Y:10.00Z:0.29 (firmware thinks it's at 117.4, 10)
Recv: ok
When I actually measure where the printhead is, I find that it's at 132.4,20, hence my G92 code.