After a bit over 2 months I finally got the miles posted to my account for the CX codeshared flights with LATAM (LA). It took a final call to the EXP desk; got an experienced agent that looked over at the travel docs I had sent and pushed it through. The miles posted immediately, and the 2 SWUs were added to the account 2 days later.

Just to clarify, the CX flights were posted to my account in just a week, the problem was with the codeshare flights that CX sold me on LA.