It's not possible to reverse (mirror) only some modules. Although GUI connections are bi-directional there is a difference between the 'inputs' and 'outputs'. e.g. you can't connect an input to another input.
Imagine you just connected two GUI pins, each set to a different value. Since connected pins share the same value, one must take priority. I'll call it the 'master'. In the old SE 1.0 'master' pins are drawn on the left, like 'inputs'. This wasn't very intuitive ('inputs' sending to 'outputs'). To fix this SynthEdit 1.1 'mirrors' all GUI pins, 'master' pins now draw on the right.
Very important point: This does not change how modules function. It is only a change in how SE's graphics are drawn, like holding a mirror up to your screen.
The second confusing change in SE 1.1 - The Container's 'Show on Parent' pin. Previously drawn on the left, this provides the ability to show and hide sub-panels. Like 'tab's or 'pages'. My mistake in putting this pin on the left is that it won't connect directly to a Patch-Mem module, so you can't save/restore what page your synth is on. Version 1.1 moves the pin to the 'other' side. The confusing part is that since 1.1 flips all GUI pins it ends up back on the left.
Some 3rd party developers wrote modules that worked with the old 'Show on Parent' pin. In SE 1.1 these modules no longer connect easily. Some seem imposible to use as intended. Unfortunatly there is no easy fix for these modules, it may be better to simply re-write them to suit SE 1.1