I was having a very similar problem. To recap what I posted in another topic, here it is.

Just as a note... I had some issues when setting up my X10 system over the weekend. It consists of 1 543 in the bedroom(another one soon in the living room), 6 appliance modules, 1 screw in, 2 lamp modules, and 3 wall switches.

I have been moving my 543 back and forth between the living room and bedroom. I noticed sometimes pretty unreliable operation of the 543 in the bedroom but it appeared to be an IR problem. The device codes would get sent but the off command would not. The red LED wouldn't flash on the 543. Yet whenever I used the hard keys on top, it worked fine.

The 543 was sitting on top of my TV underneath my remote control A/B switch. I finally moved it over to my computer desk and plugged it into a different outlet and now it works perfectly.
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So in short, try moving the IR543 around. As a precaution I did do as Chris suggests and placed double on/off commands. These are the only ones that the 543 had problems seeing.