Unbelievably they then said that you cannot include the skills test in the making up of your 45 hours
Not particularly unbelievable, as it's what's clearly written in CAP 804.
Under JAR, you only needs 45 hours to apply for the licence, ie it could include the test.
Under EASA you need to complete a course, the minimum for which is 45 hours, before the ATO presents you for test, ie the test cannot be included in the hours.
An invalid test, the ATO should have known better.