Just to make sure - you do have two Rise of Flight accounts, one for planes you have from steam, other for planes you have since forever? Each tied to different email, so that when you start rise of flight, you log in with email1 to log in with your old planes, and email2 to log in with steam planes? Because your steam account /steam DLCs have nothing to do directly with what planes you can access in the game... it's just delivery system, it's not used for DRM. All the steam products really do is give you steam version of (ordinary) RoF program, and CD-Keys that add planes you pay for to your second RoF account, the same way gift codes are used to add planes to ordinary RoF accounts.
For instance, I have forever had a RoF account, tied to email Trupobaw@wp.pl. When I log in with that account to store here and buy planes or activate gift code, they add themselves to account. I can fly these planes when I log in as Trupobaw@wp.pl into Rise of Flight.
Now, I have even older steam account, tied to email called Trup@hotmail.com. I use to log into steam and buy steam RoF and some DLCs. They are visible in steam library as available to me, but if I log into RoF program as Trupobaw@wp.pl, i get my old non-steam planes and if I log in as Trup@hotmial.com I get error. What I need to do is to make second Rise of Flight account (say, with new email SteamTrupRoF@gmail.com), then log into this site here as SteamTrupRoF@gmail.com, take CD key of my steam RoF and each of DLC I bought, and activate these CD-keys here as if it was gift code (game first, DLCs later). This adds the planes to RoF account SteamTrupRoF@gmail.com. From this point on, when I log into RoF as Trupobaw@wp.pl I get my old, non-steam planes, and when I log in with SteamTrupRoF@gmail.com I get my steam planes.
CD-keys can be obtained by right-clicking on Rise of flight on your steam library, it opens menu that has "view cd-key" option.
If you did all of above, have steam and non-steam RoF emails and accounts, have activated the CD-Keys of all your steam content on your steam-RoF account, got your planes but some of them are missing... your steam account is genuinely screwed up, send the ticket to customer support.
Are you starting ROF through Steam?
Actually, it does not matter, steam is just gift key delivery system here. I'm using both my steam and non-steam planes via the ordinary RoF program, I just choose which email I log in with. Any RoF program can be used to access contents of any RoF account. The program even recognizes if your account uses steam licence or not, and changes interface accordingly.