Salem

So while transfering large quatities of items either from stockbins or sheds or any form of storage my game client starts freezing up and transfers very slowly for example transfering 50 animal glue from a shed to inventory or vice versa takes a REALLY long time and transfers in amounts of 10-20 between pauses.

Yes limit transfer amount is turned off and it doesn't matter which client i use.

Any ideas?

EDIT: I've gone so far as to reinstalling my system thinking it had something to do with my recent windows update, even tried older versions of Java.

Bad computer, if your game is experiencing lag due to that then you experience longer transfer times. When I'm next to alot of running cementation furnaces(crazy cpu usage on that animation) then it takes a long time to take out coal from a stockbin.

I would suggest transferring goods that aren't stockbin related via a house(least amount of cpu used)

4790k ain't a bad cpu, and it was fine the other day but thanks for the suggestion

Does anyone have any ideas?

honestly, i'd throw a guess at a poor internet connection.
Here's what happens when you shift-alt-click an item:
- The client finds all similar items in that container. Note that this step finishes before the next one starts
- The client creates a 'transfer' message for each of the found items. These messages are just dumped into a FIFO queue that is emptied by a separate thread as fast as possible.

Which means that, if the pause happens inbetween batches of the same transfer shift-alt-click, then likely network issues are the cause; meaning that you don't get the server responses all at once but rather in batches. Obvious questions: how good/bad is your internet connection? Are you uploading/downloading large files while playing, which may hog the entirety of your bandwidth ?