Ok.
The thing about POP3 accounts is that they have two basic modes of operation when a email client accesses them. They can download and leave mail on the server, or they can download and delete mail from the server. Though, a recent addition on the iPad allows you to download, but not delete until some specified period of time.
So this is what 'might' be happening. The iPad is accessing the POP server, but not getting the full email, just the headers. Then your PC access the server, downloads the full email, then deletes it. When the iPad tries to access the full email later, it is no longer there to be downloaded.
My recommendation is to set the computer to leave emails after downloading, and set the iPad to delete after a reasonable period; say 30 days. In both cases you'll have to dig into the Advanced settings on both devices to make the changes.
Better would be to switch to IMAP, if you're provider will allow. If they won't, I'd consider switching your main email account to another service that does have IMAP, and only keeping the POP3 account for backup.
I really don't like POP3. It was created before most people had more than one computer to access their email, and it has not aged well. It's only good point is that it is cheaper for providers to set up and maintain; which is why so many ISPs (Internet Service Provider) have them. At least the ones where your email account is an afterthought. Unfortunately that describes most ISP's.
Another reason to have a main email address that is not from your ISP is that you won't lose that address just because you move, or decide to go with a different internet provider.
Why it's happening now? My guess is that Apple has optimized Mail a bit more, to keep it from using up too much local space on the iPad; so it's more likely to leave full emails on the server until they are needed.