** How to create such an entry:

• Option 1 (easy and common):
  Import the following VCARD:

BEGIN:VCARD
VERSION:3.0
N:User;Joe;;;
FN:Joe User
EMAIL;type=INTERNET;type=HOME:home@example.net
EMAIL;type=INTERNET;type=WORK:work@example.com
END:VCARD

This UI weirdness seem to happen for all entries where a type=HOME address appears before a type=WORK one. (The actual email address does not seem to matter, just the type)

• Option 2 (rare; I only ran into this one while trying to recover from the above import errors):
  In the web interface, create a new entry, set the Name and fill in the "Additional Email" field with "home@example.org" only (leave "Email" empty, only fill in "Additional Email"!), then save. Reopen, and add an "Email" field with "work@example.org", save. Now, the primary address for list and preview are the "home@example.org", whereas the primary address in the edit window is "work@example.org".

** How to fix the problem
Just changing either or both of the addresses does not restore correct ordering. The following process however does:
Edit the entry, cut the "Additional Email" address ("home@example.org" in this example), save. Now all three views (list, preview, and edit) agree on primary/secondary. Re-edit the entry, and paste "home@example.org" back into "Additional Email", save. The three views continue to agree.