There are internal size limitations on the amount of crap you can pile into a single Step. I think you're probably running into it. You can work around it in various ways, including splitting these 48+ actions into multiple Mapped Keys, and using Do Mapped Key Action.
However.... if you are hitting this limitation, there is a very good chance you can change your design to use many fewer Actions:
There's a super handy feature of Mapped Key Virtualization whereby if you do not provide a specific Mapped Key to virtualize, you can virtualize an entire Key Map instead of individual Mapped Keys within them. This maps every Mapped Key in one Key Map, to an identically-named Mapped Key in another Key Map. (To do this, just select a Key Map and leave out the Mapped Key to virtualize.)
So for example, in my configuration I have the following Key Maps
set up... (and I picked a couple Mapped Key names which appear in all of them, so you can follow what's going on in my example; there's more like 10 of them)
* Combat Hotkeys
** Mapped Key: DPS Rotation
** Mapped Key: Stun
* Virtual Combat
* Holy Paladin
* Blood Death Knight
* Frost Death Knight
"Combat Hotkeys" are the masters. This is where I set up the actual Hotkeys. The "DPS Rotation" mapped key has my Hokey configured (which is on my G13 input device) and simply does Do Mapped Key Action, DPS Rotation in Virtual Combat, to all windows. The others are pretty much the same but may have slightly different mechanics; "Stun" does Do Mapped Key Action, Stun in Virtual Combat, to all windows, with round-robin checked. (If everyone doesn't have a stun, I would instead use an Action Target Group for those that do.)
"Virtual Combat" does pretty much nothing. Its entire purpose is to serve as THE KEY MAP to virtualize, for any given class. On any Holy Paladin character, I virtualize "Virtual Combat" as "Holy Paladin". On any Blood Death Knight, I virtualize "Virtual Combat" as "Blood Death Knight". So each class/spec has his own definition for what Stun means, or what DPS Rotation means. The DPS Rotation for Holy Paladin is extremely different from Frost Death Knight. My Holy Paladin might just spam heals on my tank for his rotation, and my DKs of course have many abilities to DPS with.
But what I'm getting at here is that one Mapped Key Virtualization Action can implicitly be 48+ Mapped Key Virtualization Actions, by being less specific and having purposefully designed Key Maps.