There are 2 interpretations of that statement, depending on if you meant "I see a bunch of stuff in ROM that isn't showing IN Jacksprat or JackFlash."
#1:
Things WILL show up in ROM that JS/JF doesn't see. If you couldn't see it in JF/JS, then you haven't moved it - you wouldn't be able to.
did you take a "snapshot" of your system before spratting anything? If so you're in good shape. Delete extra languages, delete proggies you don't want (with remnants if possible, like Docs 2 Go) . . . prepare or "initialize" the created flash area to be ready to accept incoming new stuff, move ACCEPTABLE programs to flash, and soft reset.
That should be it. You can put agendus in flash . . . but NOT icons, databases, AN Info, IambicLicenses (if your Agendus/Iambic stuff is newer), etc. ONLY the .prc itself. Brayder suggested to me that I did NOT put Agendus in flash . . . but I did anyway when I was using it, and it was fine. HOwver, thta was an older 6.0 and subsequent 8.06 version - the later ones are so convaluted (v9, v10, whatever they're up to now) and "interactive" that I douibt I'd risk it.
#2: You want to put JS/JF in Flash. You can't do that; they have to remain in RAM. I'm pretty sure you meant #1 above, as there's a message if you try this #2.
Hope this helps - / p