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In both TPM and ROTS Jedi are stopped cold by ray shields. However in the new Clone Wars series it is seen that Jedi easily pass through theater shields. As far as I know the it is possible to penetrate theater shields due to their interaction with the ground. Wouldn't ray shields also have this effect?

Also IIRC it was said in the AOTC ICS that clone armor protected against the effects of passing through theater shields. It would seem possible that Jedi are able to pass through the shields due to their ability to dissipate energy, however this would not explain how they were stopped by ray shields in other settings.

I think this qualifies as shields are more complicated then you're giving them credit. The TPM and RotS incident I recall is those weird forcefield gates and when Grievous literally orders shields to trap them. Both are highly concentrated setups. Theatre shields on the other hand are very spread out setups that in practice are more like a F-you to artillery/air support. It is entirely conceivable different compromises are in place for these two widely different applications.

The simplest answer along you lines could just be:
Theatre shield intensity < Jedi ability to mitigate
Localized concentrated shield intensity > Jedi ability to mitigate