I've taken a look at the source code for the 1.6.2 synaptics driver, and there is definitely code in there to support setting "SoftButtonAreas".
So I am going to guess that it is being initialized properly, then being changed later.
The fact that it worked one time is consistent with that guess.
Please post the output of this command (note the leading dot and capital 'S' in the filename):
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cat /root/.flSynclient
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mv /root/.flSynclient /root/.flSynclient.hid