1: If the node would be created more than 180 degrees around the moon's orbit from your current location, it is instead created at your current location, pointing in weird directions.

2: Even when created in the correct location, the post-burn altitude shown on the map is much lower than the desired altitude that was entered.

Reproduction:

Put a ship in circular Mun orbit. (Or use https://dl.dropboxusercontent.com/u/203721/Mun_Orbit_persistent.sfs)
Open maneuver planner, select return from moon, enter 100km, click Go.
Switch to "change the last node" mode.
Time accelerate to 50x or so and click Go repeatedly, observing changes in node placement and predicted orbit.
When node is correctly placed, look at Kerbin: Periapsis is not shown, as entering 100km results in a predicted collision course.
Enter 800km and click Go from an orbital position where the node will be placed correctly.
Predicted periapsis is now shown, but with a much lower altitude than 800km.

Expected behavior: Node is always placed in approximately the same location, and predicted periapsis after maneuver matches the entered altitude.

1. Thanks, I see what is causing this and will fix it.
2. Yes, currently the calculation of how to hit the target periapsis is only approximate. It is particularly bad for the Mun because its SoI is quite large. At some point I will look at improving the accuracy of the calculation. For the moment, as you found, you can twiddle the target periapsis until it actually gives you the periapsis you want.