So I flew a codeshare flight on UA about 3 months ago and apparently my Onepass number wasn't associated with it (Which was strange since the first CO leg of the trip had it on my ticket and it was on the same reservation). I sent in my boarding pass and they replied that it would take about 3 weeks to process. About 4 weeks passed and nothing showed up in my account, so I sent another message to customer service to see what the status was. They said that they are working with the partner and the miles should post within two weeks. Well 3 weeks have passed since then and still no miles. I sent another message to customer service asking the status, but haven't received a response. Any suggestions on what to do next? Is calling in going to do any good? This seems like a ridiculously long time to credit miles.

Yes, in these cases, it can take up to two months for the miles to credit.
Its still worthwhile to call and ask whats going on.

I had the same situation twice this year. The miles posted abuot 6/7 weeks after I made the initial request.