I worked on my pilsner for years before I got it right. My final hurdle was water chemistry. That said, I just dumped a batch due to underpitched/stressed yeast and/or possibly infection. It took an entire week to show signs of fermentation. When finished it was terrible, like beginner hooch. The only thing I did different was the yeast. I didn't propagate or even ensure viability, just dumped a stored slurry. Well that's what you get when you're in a rush. I've made plenty of great pilsners using a stir plate and plenty more using SNS. I'd look beyond your yeast method, are you pitching enough? How's your sanitation? Were these tried and true recipes that you used before, recipes sometimes need to be tweaked to work on your brew system. Are you checking your pH and mineralization? Pick a recipe/style and keep working it until you get it right.
I believe I'm pitching enough yeast; in fact I think I'm pitching too much. My process has been to use Mr. Malty's viability percentage combined with brewunited's yeast calculator. I wonder if the combination of the two leads me to pitching more than I realize.
As for sanitation, I believe my method is sound. I admit I don't freak out about sanitation like I used to, but I am mindful of it during my entire process.
Most of the recipes I've brewed have been taken from Brewing Classic Styles, but scaled for batch size and my mash efficiency. Would these recipes need to be tweaked to produce good beer?
As for water, I use beersmith's water calculator set for distilled water. But I actually use RO water from a dispensing machine at the front of my local Publix grocery store. Actual mash pH has always been fairly close to beersmith calculations.