There is a previous thread on the TPMS and the conclusion was that it is a very sophisticated system and likely to be more accurate than any maunal pressure guage (unless you have a faulty sensor of course). Not my words but those of some qualified people working in the field of electronics and automobile TPMS.
The gist of it is that the TPMS system on BMW's compensates for temperature and shows on the TFT the pressure adjusted to be what it would be if the outside temperature\tyre was 20c (I think 20c is the temp at which the tyres should be set at the recommended pressures 2.5bar and 2.9bar on the 1250gs).
Because of the temperature compensation the TPMS may always show slightly different to a pressure guage, unless the tyres and air temp are 20c.
but it's not necessarily the TPMS that's wrong (unless its faulty) its your guage misreading because of the temp.
If the pressures are incorrect it also shows on the TFT what pressure adjustments should be made to get the tyres to the correct setting at the current air\tyre temp. e.g. if it sees the front tyre is over inflated by 0.5 bar it will show -0.5bar adjustment to get it to the correct setting. So, regardless of the air temperature, & temp of your tyre, when you put your tyre pressures guage on take the reading and just drop it by 0.5bar. Ignore what the actual pressure reading is on your guage just make sure it's 0.5 bar less than when you first put the guage on.
When the bike has just been ridden and the tyres are hot the pressure with a manual guage could easily be .3 or .4bar higher than when at 20c. If you set them when hot, to the readings on your guage, when the tyres cool they will be wrong, but if you do as the TFT is telling you and drop (or add) to whatever your guage shows by the amount the TFT says, they should then be correct at 20c.
Hope all that gobbledegook makes some sense but don't shoot the messenger.