Magento Deadlock, needs trouble shooting

Our magento store is not working properly, it was working fine and we aren't able to track the issues down to the installation of any particular extension or update but our host says it may be related to one of our extensions not being compatible with another. What is happening is you place an order with paypal, pay and then you can return to the site and the site gives you an order id and everything as if the transaction has gone through but the customer nor the admin ever get a new order email and if logged in as the customer it will say you have placed no orders. When you view the order in Sales > Orders it shows up but is marked Pending Payment. To see if this was a paypal only issue we enabled the check/money order payment method. When you place an order with the check/money order payment method it also goes through the process with no errors and it does send you the new order email as well as send the admin the new order email and the order shows up in Sales > Orders in the magento admin panel like it should but if logged in as the customer it says you have placed no orders still. We tried google checkout and google checkout does the same thing as paypal, even after paid no order emails come out. We have already tried searching google for a fix and we hired a developer that was unable to determine the problem after hours of fixes and trying to place orders. The last dev said this "And please make sure that the person knows its a magento database deadlock and not drupal. And tell them not to use the solutions found in google." We have an extension called M2EPro that does ebay > magento syncing. This problem doesn't seem to be effecting our ability to do business on ebay, just the website orders are effected. We are really looking for someone who has dealt with this type of issue before and thinks they can fix it very quickly it hopefully being a very simple issue. Since this store is live and having inventory added as well as syncing ebay with 43,000 products it is crucial that you know what you are doing and back anything up before you make changes. Thank you, please message me with any questions you have.