Is there a setting for the block behaviour? I've never used IDEC, but in Siemens logo for example, you can choose the behaviour of the latch (as in Reset over Set or Set over Reset).
The only other thing I can see that may be giving you trouble is the way the instructions are processed. The RS that doesn't work has a signal coming from a logic block that hasn't been processed yet. This could be it. Have you tried putting that signal into a memory location and then read from a memory location into that RS block?
This seems an awful lot like the Siemens Logo IDE, and from what little I've read it has some rules about how the signals are mapped. Have a go at it.