Fix PME load balancing skipping a setup

Fix PME load balancing skipping a setup

During stage 0 of the PME tuning we only time every second setup.
In stage 1 only a reduced range of setups is considered. If the tpr
setup (setup index 0) was not part of this reduced range, the first
setup in the range would never be timed. This could lead to choosing
a non-bonded cut-off that was longer than optimal.

Fixes #1880

Also fixed two conditionals (but this had no effect on the settings).

Change-Id: Id9f361d23e3294e41553b39ae8e8f37ceb80bbe5