The only way I know around this is to download an app and install it directly to the SD Card, bypassing installing it on the phones built in storage. The update issue only seems to come about when an app was originally downloaded and installed on the phones true "Internal" storage and then moved over to the card after it was made into "Internal" storage. I have not heard of it happening after uninstalling the app completely and then downloading it directly to the card and installing it there.
Of course the card will have to have been converted over to be "Internal" storage for it to accept apps before this can happen.