Did you recently upgrade from the GNS 430  to the IFD?

There was an upgrade but it was years ago.

The question is, if the IFD's have current navdata, does the EX5000 also need to have current navdata in order to show a flight plan entered on the IFD?

I've never flown without updated databases on both the EX5000 or IFD, so my explanation here is not based upon any personal experience where I've witnessed the problem you describe. Nevertheless I think I understand what your problem may be.

Both the IFDs and the EX5000 require Jepp navdata to map FAA published waypoints.  The boxes alone do not come equipped with the locations of any of those waypoints.  The boxes are a blank slate that Jepp navdata writes to.

The EX5000 has a map that is independent of any database, and if provided coordinates from a GPS, it can plot a location accurately on its map.  The IFD's GPS will provide coordinates for your aircraft that places your aircraft symbol at the correct location on the EX5000 map.  This does not require Jepp navdata to accomplish, since latitude and longitude are built into any map and do not require navdata to accurately display a location that is fixed by those coordinates.  Same goes for waypoints you enter manually into the IFD with coordinates you provide.

But plotting routes that are defined by FAA published waypoints (fixes, navaids, airports, etc) requires Jepp navdata info.  You can't load a route made up of FAA published waypoints into an IFD that does not have Jepp navdata, because without it the IFD cannot recognize the waypoints you attempt to load.  You don't have that problem, because your IFD has current Jepp navdata loaded.

Your IFD uploads your route to the EX5000, and if the EX5000 also has current Jepp navdata installed, it will recognize the waypoints - all of which will already be displayed on its map anyway - and plot your route.  It sounds like your EX5000 has Jepp navdata that is so out of date, or missing entirely, that it makes it unable to plot a route from your IFD that has published waypoints that your EX5000's database does not have.  If your route has any waypoints you entered manually, the EX5000 should be able to display those, but will not be able to plot a route between those and any published waypoints on your route that are not in the EX5000 database.

The PFD's HSI display also shows the routing, but the PFD does not have the capability to maintain its own Jepp navdata.  Therefore, unlike the EX5000 or IFD, the PFD's HSI map has no ability to display nearby airports and waypoints.  The PFD can only display the mapped route data it gets from the EX5000.  So if the EX5000 cannot display the route for lack of accurate navdata, then neither can your PFD.

OK. Navdata updated along with charts. Works better, but still some problems:

1)I enter a flight plan on one of the synched 440's. I have to activate it several times (or on both 440's) before it will appear on the Entegra. It always appears right away on the IFD100

2)With an active flight plan showing on the Entegra [i.e. current (magenta) leg, next (magenta/white) leg, future (white) legs] if I add a way point on a 440, all legs disappear from the Entegra. They display correctly on the IFD100.

3) If I select OBS on a 440, the displays (magenta DTK, green CDI) on the PFD and MFD start jumping around. I can select a course but the display jumps around quite a bit. I've tried doing this for several way points and its very repeatable. This only happens for a GPS waypoint: if I select VLOC to a VOR, the display is steady. The display on the IFD100 is always steady and correct.

Any suggestions as to where to look for a solution?

Check the status of the EX5000 MFD software.  Mine is 8.1.1, which works.  IFD's should both have the same software loaded.  Mine was 10.2.3.1, and it worked fine with the MFD.  If they are out of date, have your avionics shop bring them up to date.  Your avionics shop will know how to check the status.  You can also check the software status yourself - check your manuals for details.

If all your software is up to date, there must be some kind of problem with your boxes and/or your installation.  That will require assistance from Avidyne tech support, as well as your avionics shop most likely.  Good luck!

We're also running 8.1.1 and 10.2.3.1. Here's a video we made:

https://youtu.be/q2ElLjUBLVQ

We have a call into Avidyne and will visit a shop in a few days. Seems like the problem stems from the 440's since both IFD100 and EX5000 behave similarly. Not sure, but I think both 440's behave the same way (i.e. when one or the other is turned off).

If you fly far enough north or south, it's the only way to go.  Near the mag poles, flying by mag compass is nuts.  So it makes sense to make an airplane capable of that navigation, since planes after all are not limited in where they can fly. 

Why anyone would set up the unit like that and give it to you?  Probably a oversight by your avionics shop.  Also a lesson in the value of studying the entire pilot manual, make notes, and learn the box and all its settings.  Then, figure out how you want yours configured, and then go to your plane and make sure they are set up that way.  That helps limit "why is it doing that?" scenarios.

Glad you got it sorted out.