People have said the 2 apps share cookies. Just use seperate IDs. It feels a bit much at first but then you get used to it and especially if you have your main ID not for ebay, it stops you from making silly mistakes. Like say you were drunk and decided to see how your sales were going etc.
I used to use the clear cookies, change IP method.. but that was just confusing afterawhile.
Now I used the change user ID method.. I can save the passwords in there, so I won't have to type any username in there really.. i just clik log in and it isbe automatically setup for me.
I have been using the same user profile for all of my ebay and paypal accounts.
And i have never had an account linked and i have been selling for over 6 months
I am using firefox and i have set to "erase private data + cookies" every time i close
I also have flash cookies disabled. everytime i start firefox for an ebay session i restart my router and than i restart it again when i finish just incase i forget. I use pop peeper to check my emails and i have set it so that my emails are shown in just rich text