Welcome to the forum.

If this were the mk4 type system I'd say that either the GPS antenna is duff or the Trimble unit (inside the navigation computer is faulty).

However you say that these have been replaced with new ones.

So the fault must lay else where, are the roads where theses "black spots" are good? or are they bumpy and have pot holes etc (something that may jar the suspension or body?) as this could be the fault, maybe one of the ABS/speed sensors in duff?

These work in conjunction with the nav system to give you your dead reckoning (for when you lose satellite signals), if one is faulty then this could put the nav unit into a funny mode where by the road speed does not match that of the satellite GPS speed (very unlikely but possible).

Also check the main clocks binnical out if this has a fault then this could also effect the nav system.

Also try an update to the nav system as its possible that the on-board Trimble unit "forgets" where the satellites are (check the almanac for this), and this can take a while to repopulate.

Personally it sounds like the antenna is duff.

I'd get a cheap £6 SMB GPS antenna off ebay and plug it in to the nav unit and leave it on the dash and see what happens.

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Sept 03, M3, Silver Grey. Retro-fits: Modded Mk4 DVD Drive, OEM Bluetooth, VR Control, Rainbow Speaker Upgrade, Sony SOT Amp, HK Sub, CCFL, Intravee II, NightMode.