Try letting the glow plugs go a little longer after the light goes out. Sometimes if I hit the key right after the light goes out, the engine runs a little rough for a few seconds. I usually wait 3-5 seconds after the light goes out to start the engine and it will run just fine on startup. I also have new Bosch plugs but the controller is the same that was on the car before.

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1991 F250 super-cab 7.3 IDI. (rebuilt by me) Banks Sidewinder turbo, hydroboost brakes, new IP and injectors.
2003 S430 - 107K
1983 300SD - Tanoshii - mostly restored ~400K+.
1983 300SD - Good interior. Engine finally tamed ~250K.
Monark Nozzle Install Video - http://tinyurl.com/ptd2tge