It's true that DR doesn't help against a grapple check. However, note in the description of the mind flayer's abilities in the MM:
Improved Grab (Ex): To use this ability, the mind flayer must hit a Small to Large creature with its tentacle attack. ... If it gets a hold, it attaches the tentacle to the opponent's head.
After a successful grab, the mind flayer can try to attach its remaining tentacles with a single grapple check.
To me, that suggests that the mind flayer's Improved Grab would not work on a creature with DR, since the ability requires that the mind flayer hit with its normal attack first. Thus, the Extract ability wouldn't come into play either, since _that_ requires all tentacles to be attached. If it was already grappling, however (ie it managed to make a grapple check normally) then it could make grapple checks as normal to attach all its tentacles.