Thanks for the documentation links.
I've gone through some of them, but I'll go through the rest this weekend.
Here's an example from the logs.. we couldn't do some operations on the website, so I had to kill the connection (unfortunately).
2016-12-28 17:36:18 MySQL_Session.cpp:2173:handler(): [WARNING] Retrying query.
2016-12-28 17:36:48 MySQL_Session.cpp:2173:handler(): [WARNING] Retrying query.
2016-12-28 17:36:58 MySQL_Session.cpp:2173:handler(): [WARNING] Retrying query.
2016-12-28 17:37:08 MySQL_Session.cpp:2173:handler(): [WARNING] Retrying query.
2016-12-28 17:37:18 MySQL_Session.cpp:2173:handler(): [WARNING] Retrying query.
As for the transactions, I guessed that setting transaction_persistent to 1 for the user would disable the query routing.
Are you available for paid consultation and assistance in getting proxysql set up correctly?