There are notes elsewhere in the forum observing and expressing this, for what it's worth.
(Being a very hard thing to prove cause and effect to Plarium. Needing to prove when it went on, for how long, when it is off, and that no battles occurred in the mean time causing the shield to drop.)
It does not make sense that it is particular to 3 day shields - the shield expiry timer is the shield expiry time, regardless of the combination of boosts applied to get there. I certainly cannot dispute the idea though - however much it doesn't make sense. The proof is in your pudding, as it were.
If you or your mates are willing, it would be interesting to hear of any reports of one(s) applying a 3 day shield, and others applying 3 1-day shields at the same time - with the former dropping early and the latter not.
In the mean time, please have you and your mates consider taking screen shots of shields being applied (before / after 3-day shield inventory count, I suppose), shield time effected, shield not in effect, and order battle reports [being a short list, as it were] showing no attacks or raids initiated in the interim.
You could even post them here then do Menu / Ask a question, or http://support-portal.plarium.com/ticketcreator/throne/en?devicelocale=en&spGame=throne-web pointing them to that post.
You would be doing all of us a great service to track down these mysterious shield drops so that Plarium can find and fix the problem. Such deeply irritate everyone.
By posting here, perhaps many can collectively accumulate evidence that helps point Plarium to the particulars sooner rather than later.