Hi,
I've been having a similar problem and this happened to me twice now that the playmaker menus and panels disappear. I did not swap from a project that wasn't using playmaker, such as mentioned above, but instead it has happened at random when I have opened up my project that had been working fine with playmaker up until the point I quit unity the day before.
The first time I fixed it by making an export unity package of all my assets and any required playmaker scripts (eg globals) and Unity input setup etc. Then I created a new project by importing all the assets packages I had in my original project, then imported my custom package and then it seemed to work with play maker again until just now.
I can't afford to lose a big chunk of day every now and then at random in my development so it would be good to know what is going on to help cut down the impact.
I haven't upgraded to the latest unity 3.5.0f5 and I'm on the Mac, if you think I should upgrade let me know.
Any other tip or suggestions that might explain it?
Also how do I refresh/reload a layout? The layout I created which showed the playmaker windows as well as the usual unity panels is still available to me to select. Though if I reselect it in the drop down it doesn't show now the playmaker panels, just the unity ones.
Any help would be appreciated as I'm fairly new to this and there are deadlines involved

Thanks in advance,
Hermit Studio