They mostly fixed it after Select Executive got rolled out. I suspect (quite strongly, indeed) that someone figured out that the extra 500-750 points (500 normally, 750 during Double Days) you'd get per upgrade with what was, at the time, a pack of five upgrades for 10k points (it's now four, but it was five at the time) was potentially slightly broken (during Double Days, you'd get 3750 points back from the coupons...and kick out an additional coupon to boot), especially when combined with the Select Executive coupons (which you'd get every 3000 TQPs...so you'd be getting a coupon for every four city pair-qualified Acela First legs regardless of how you got there, giving you a fifth upgrade gratis) [1].
You didn't /quite/ have a feedback loop, but it was close enough to one to merit closing: The effective points recovery on points spending was a real potential revenue killer among the Acela commuter brigade.
[1] So, consider the following scenario under regular circumstances: I get my four "welcome upgrades". I use them to upgrade on the Acela. I get 1500 points per leg plus any credit card spend under normal circumstances (thus 6000 points, 3000 TQPs) and a free upgrade card as a result. If we're on low bucket on the old credit card, we're now at 7200 points earned. I upgrade again (so now we're at 7500/3750 plus the CC...probably another 1500, so 9000 overall)...and IIRC with the CC you'd get 5% back on the redemption for upgrade cards. Basically, if you have ANY other travel in regular season you'd be perpetually pulling 48-hour upgrades. In Double Days, this would get even worse: 10,200 points earned (9000 for four Acela First legs, 1200 for CC spend) gets you another five upgrades for 9500 plus a free upgrade (for the 3000 TQPs). Using the earned upgrade first, you're now at 12,750 points in and 9500 out (so net 3250). "Earn Select Executive, Never Pay for Acela First and get a 50% discount on your required status renewal spend" is not a winning model.