That is probably because all three are at different LFE levels.
It is possible the the Discwasher and THX discs have LFE tone levels around -20dB Ref and the pre-amp has tone level at -10dB Ref, therefore making the SPL higher for the pre-amp. This is not uncommon even between calibration discs. For instance, DVE and Avia have LFE test tone at +10dB compared to other channels So, when using the these disc, one needs to calibrate channels for 75dB SPL and LFE at 85dB SPL. This
article helps understand the thought process involved in making the LFE test tone at +10dB when compated to the other channels.
Whichever source you use for generating the test tones, the net effect is the same, they provide you the ability to make sure that all your channels are level matched. To find out the setting for your pre-amp's master volume control that gives you reference levels, the THX tones need to be played to achieve 75dB.
I personally prefer to use a disc since my Denon AVR's test tone levels are not controlled by the master volume control. This way, I know that my master volume needs to be a "-19dB" for my SPL meter to read 75dB, is it is therefore the setting at which I have Ref levels.