It is not uncommon for transactions that are reported in the shopping admin panel to be missing from GA. GA is a trend analysis tool, and as such cannot be expected to be 100% accurate.
However, if the variance is greater than 5%, you probably have an issue with the tracking code. This could be for a number of reasons:
If more than 10% of transactions are missing from GA, then there is likely to be a bigger issue and this should be investigated by running a number of test transactions with a debugger like Fiddler to ensure the right data is sent to Google Analytics every time.
Thanks for your response. I knew GA was inaccurate but not to that degree.
Would orders on Amazon, create a Magento transaction id? If so, it could explain the difference?
Do cancellations create transaction ids?
I'm looking for reasons why this number is higher than actual orders.
If the database is clustered, ids will be skipped depending on which nodes are doing the writing to the database. Are the ids sequential otherwise?