There is a bug in Modest default email client. The contents of emails are cached in the internal memory. But when you remove these emails, this cached information stays present. So modest will slowly fill up your internal memory, even when you remove these emails.

So I got exactly the same problem as you. But after removing these cached information about 50Mb memory was free again!

How to remove these cached emails?

From X terminal, goto the map:

cd /home/user/.modest/cache/mail/pop/<user_name>/cache/

(where <user_name> is the user name of your email account)

Now remove all cached mails:

rm -rf *

(be carefull using this command, you have to be sure you are in the correct map, removing all directories cannot be undone).

Because I did not want to clean up this cache over and over again, I made a symbol link from /home/user/.modest/cache/mail/pop to my external memory card. Works perfectly.