Sounds like one or the other is not syncing. Need to know how your email is set up before I can really help beyond generic suggestions.
1. Remove the email from your account using either your computer or the website for your email (if it has one)
2. Remove the Mail entry - delete the whole account - from the iPad. This will delete the data. Then, sync without adding it back in. Then, go ahead and resetup the email account on the iPad.
Some things to think about.
Option A:
1. Use Gmail for your primary email account. They fully support IMAP - better than POP3.
2. Gmail allows you to connect via the Exchange method. This will allow you to fully sync Calendars, Contacts and Email. This way, you will always be synced up no matter what device you are using.
Option B:
1. Sign up for a full Microsoft Exchange server account (I use 1and1.com) - Not free, but I have had mine for 5 years now and have had flawless service and have been able to keep 4 different devices fully synced up nearly instantly.
2. On your PC you can use full-blown Outlook and all of its functionality. Powerful program.
3. When you are not at your PC or iPad, you can use a web browser to access your email.
