how do I use pretreatment method on agilent 1200 using empower FR5

I have an instrument method trying to run a pretreatment method on an agilent 1200 via empower. Using empower FR2 this ran smoothly, but after upgrading to empower FR5, the pretreatment method gets ignored altogether. When using the handheld device (gameboy) to open the method, there's an "injection mode" setting that can be changed. The empower programmed method looks like it defaults to an injection mode of "standard", but it needs to be changed to "injector program" to actually recognize and run the programmed pretreatment sequence. 

I don't see any way of altering the injection mode via empower software. The 1260 and 1290 series seem to have a checkbox that must be clicked to recognize the pretreatment sequence, but I see nothing like that with a 1200 series. I can't save the method that has been altered via the handheld device back into empower, and unfortunately, I have to run everything through empower. Has anyone run into a problem such as this?

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