I have found polycarbonate is funny stuff to work with, it's totally different to PMMA (perspex). You need to ensure your cutting tools are razor sharp, because this plastic is softer than acrylic, and thus tends to drag on the tool a little. Also worth mentioning that I find clear plastics can vary a lot in quality. If you want consistency, then try and stick with good brand names- e.g. GE's Lexan, Makrolon
A suitable alternative is PVC- easier to machine, cheaper, and perfectly suitable for piston tanks. You can also use aluminium (although be mindful of anodic corrosion), and I've even seen G10 epoxy sheet used.