This maybe resolved ... and I don't think this is an Aqua Mail issue. I'll detail this here, should anyone else need to know.
My mail is being processed and transported by cPanel but handled locally by ZOHO mail, a third party email client. Digging deep in my settings, I found a little check-box Delete mail once downloaded from server IT was checked meaning that zoho was not only handling my mail, but deleting everything it was collecting from the server. Zoho has it's own servers and relays all content to my local email client. Even with my local computer off, zoho is still polling, collecting and deleting mail from the main cPanel mail server.
RESULT. Any mail on my cPanel server was being deleted after zoho collected, therefore every time aqua mail was polling the cPanel server, there was nothing there. The only time I received mail was when I sent mail to myself FROM Aqua Mail. This seems to trigger an immediate email push that intercepted zoho's polling on the server.
So, unchecking the Delete mail once downloaded from server seems to have removed this problem and I'm receiving mail using Aqua Mail settings that previously failed to work.
Thank-you Tomas and Vasilyev for your help and input and I hope this explanation makes sense and may help others.
Let me know if there is something I may have missed that could remedy this better?