Your obversation about the difference in level between guitar/amp and line sounds correct. The more signal the PF gets, the better the signal-noise ratio will be, too. Just make sure both input and output switches match, but it sounds like you have done so already.
It does seem odd that the PF isn't getting enough signal to use the tuner. I've got an Orange Rocker 30, but that doesn't have a loop, so I can't directly compare. I do have several amps with either parallel or series loops (or both). The send level of many series loops is controlled by the gain or volume controls, so maybe turning up a little will help (if that's an option in your practice space).
Does the PF get enough signal to use the tuner when you plug directly into it, before the amplifier? If not, it may be the PF that has the problem. I don't want to see you send the PF off for repairs if that's not definitely where the problem is, though, you know? Basically, just try it in every possible configuration. If the problem is always there, it may be the PF. If the problem only occurs in some configurations and not others, the problem is probably not the PF.
What are your settings for Bypass Type and Killdry? What about Global Mix? Moving back and forth between series (Rockerverb) and parallel (Earforce) loops usually requires changes to several settings, so maybe the problem's related to that. You did say that the volume drop occurs on every preset, and not just some but not others, right?
The Output Level in V3 can be adjusted up to +6db, so that may be enough to solve your problem, too. From the PF Update page…
"In PLAY Mode, holding down the Left Footswitch for 2 seconds from Bypass state puts the unit into Active and also puts the unit into Preset O/P Level Adjust Mode. While the footswitch is pressed and held the display will show “OP 0dB” (default). While continuing to hold the footswitch down you can optionally turn the Encoder Knob to adjust Preset Output Level from –20dB to +6dB in 1dB increments. Preset must be saved or this adjustment will be lost when another Preset is loaded. (Preset Level Adjust Mode functions the same way in BANK Mode by pressing and holding the Left or Middle Footswitch from Bypass state.)"