I had a similar issue. First, check you mailbox settings to verify how many messages it is setup to show (I believe that 200 is maximum).
My experience is that the Ipod Touch does not display the most recent messages without deleting some of the older messages that it intially loads in. I suspect that the Ipod Touch may have a memory/storage limit that may be impacted by the size of the email and attachments (if any). Unfortunately, I know of no way to delete the older messages other than one at time using the edit function. You will have to delete the older messages from your mailbox and then delete them a second time from your trash bin (the messages will only be deleted from the Ipod not the email server unless you have set it up to do so--check your advanced mailbox settings).
Once you have deleted a number of older messages from both the mailbox and the trash bin, update your mailbox to load in the more recent messages. You may need to scroll to the bottom of your email messages to see if there is a prompt to receive the next group of messages. You may also have to go through this process of deleting older messages several times before you are able to load your most recent messages.