i've never had a problem with emu...and i've been using it for over 10 years on a 5efte with ct9, td04 and various versions of td05/vf35/etc with different injectors starlet 295cc/mazda 360cc & 460cc/subaru565cc
i've seen this 100% duty in logs and it never affected anything---usually in 1st, 2nd and 3rd gears...it tends to smooth out in 4th gear.
now i can't say for certain, but i suspect it has to do with the injector scaling parameters used and then that its a piggyback and is altering the stock ecu signals...tuners will tune emu/emb differently, in the scaling section some input original injector sizes and new injector sizes, some input lag times for the new and old injectors, some input both (which may differ), some input none, some input a combination...then proceed to tune accordingly....this could affect what you see in logging and how the emu/emb final fueling/ignition tune comes out. This aside, my car drives and operates like a stock car with this piggyback, the way it should be with any ecu ---no jerking/juddering, no running rich on idle or lean in the revs, no unexplainable map loss, etc
10 plus years ago emanage was a good option for me over the preprogammed ecus (blitz, jam, sard, etc which can't be tuned and were/are very much overpriced), the very good/expensive standalones or cheaper/developing standalones at that time...and most importantly to me at the time, my tuner knew how to properly install and tune emanage (this is extremely important for any ecu you plan to choose and run in your car) and it used the stock sensors. Nowadays with the wider assortment and more affordable/developed standalones available which can use stock sensors, if i had to do it again, i'd probably choose one of these over emu. But as stated earlier, if it working, leave it alone---so emu remains for me.