I came across this issue when I was trying to find out what the periapsis should be over KSC if you want to land there. I noticed the orbit and location of my ship changing each time I tried testing the mission.
KSP Version: v18.104.22.1689 (WindowsPlayer x64) en-us
What Happens: Orbits created in Mission Builder do not save correctly.
Mods /Add-Ons: All Stock (Fresh Install)
Steps to Replicate:
1) Open Mission Builder
2) Open Mission Brief - rename - click ok
3) Select 'Spawn Vessel' node
4) Choose 'Creator Built'
5) Choose 'Create New Vessel'
6) Select 'Take me to the VAB'
7) Select 'Mk1 Command Pod'
8) Leave - Click 'Save and Continue'
9) Select 'Spawn Vessel' node
10) Choose 'Untitled Space Craft' from 'Please select a craft' dropdown
11) Choose 'In Orbit' from 'Situation' dropdown
12) Change Periapsis to 38000
13) Change Apoapsis to 100000
14) Change Arg. of Periapsis to 196 degrees
15) Change Target of Mean Anomaly to 260 degrees
16) Click 'Assign Crew'
17) Assign Jebediah Kerman to the Mk1 - click ok
18) Save and Test Mission
19) Return to Mission Builder
20) Click 'Spawn Vessel' node
21) Test Mission
22) Finish the test mission by crashing
23) Return to Mission Builder - End Test
24) Click 'Spawn Vessel' node
Note 1 - step 18) The purpose for this is to crash near KSC
Note 2 - step 18) You will notice the Target of Mean Anomaly is not 260 degrees
Note 3 - step 18) You will notice the Periapsis where it should be
Note 4 - step 20) You will notice Target Mean Anomaly is still set to 260 degrees, but the world viewer does not reflect this
Note 5 - step 20) Changing Target Mean Anomaly from and to 260 degrees updates the world viewer
Note 6 - step 22) Mission time should finish around T+ 0y, 0d, 00:18:45
Note 7 - step 24) You'll notice the Periapsis is no longer above the KSC
Note 8 - step 24) Even though Mission Start Time is set to 0 time seems to have jumped forward for the orbit and world viewer after testing.
Saving and playing a mission instead of just testing yields the same results of the last test.
Other Notes/Pictures/Log Files: Pictures of 3 different Map Views with the same settings.