No one is having the same problem?
It's better to save the Mystery, than surrender to the secret...
I'm having problems with flying allies as well. The ally characters fly some in the patrols I'm using them in, but as allies they are suddenly ground-bound since the last patch.
I would have tested this on the Test Server, but the character copy tool was down for days, and when it finally worked, I realized that transferring a current character did not unlock all the stuff I had unlocked on Live, so I had to earn tickets again before I could test the mission as it exists on Live.
By the time I got that accomplished, the patch had gone live, and the player base is now experiencing the new bugs in my arcs at the same time I am. 
I'm wondering if this has something to do with the new ranged attacks. Before, my allies would chase guys into the sky, which was cool. Now... it's not.
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Check... and Mate (poster) - Arc ID# 15095 (comments)
Invasion on Earth BX1132! (poster 1) - (poster 2) - Arc ID# 98943 (comments)
Global @ARH
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Characters with fly powers only fly if they have no other means of reaching the enemy or following the ally. They don't simply constantly fly. Have you tested this by breaking line of sight by flying up near the ceiling or out of range yourself?
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Well, My ally had fly and when I would fly she would follow NOW all she does is try to jump to me if there is a tree or something near by other wise she runs in circles...
although the partol flying mobs are now flying again when they retreat...
It's better to save the Mystery, than surrender to the secret...
Yeah, I'm having the same trouble too. I'm using some pre-"fix" allies and some new ones. All should fly (pre-fix ones used to) none do under ANY circumstances. This includes in outdoor zones. They are now MUCH more likely to loose me. Part of "tricks" of some of my stories is knowing who to rescue 1st, and how well they can follow has a lot to do with that. Plus if they can fly when following you they are more likely to avoid unnecessary mobs.
I hope the devs are paying attention to this "fix". I mean I am patient if it takes a while to resolve this, but I hope they realize there IS a problem with the most recent tweak to fly and that is not working right.
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I just got a reply to the in-game support ticket I sent on this issue, and it seemed like they had never heard of it before. I explained it more in depth in my email reply.
I realize support gets a lot of tickets that are not really bugs, or something the player has misunderstood (I myself have submitted a thing or two that I later found to be an error on my part). And I realize they have to have stock responses to weed those out and save time.
But this is a known issue-- at least to anyone who has flying allies in their arcs-- and for them to respond with a "must be your arc" message just sets me to grinding my teeth. And until we get an official response to this, I am going to bug it in-game every time we get a new patch/issue that does not fix this.
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Check... and Mate (poster) - Arc ID# 15095 (comments)
Invasion on Earth BX1132! (poster 1) - (poster 2) - Arc ID# 98943 (comments)
Global @ARH
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After this so called fix... the characters in my arc no longer can fly I had a mob with flight and an ally with flight now no flying... The ally had reflections and she was able to fly now all she does is jump no flying... anyone having this problem and if so (silly question) are there any plans to fix this?
It's better to save the Mystery, than surrender to the secret...