Yes you are making your cylinders to small. There is a quant limit on how small a block can be. Cylinders reach that limit much quicker because of the angled surfaces.
you really only have a few options:
Scale up your entire level so the cylinders do not have to be so small.
Use square bars, blocks scale down further then cylinders.
Use models for bars.
Simulate bars using sprites or textures.
Using cylinders for bars should actually be your last choice. It would jack up your portal count very quickly, giving you an unnecessarily large level.
models made in med or some other modeler would probably be your best choice. Use blocks if you do not know how to model.
Good luck with your deadline!