Yeah, you are using the v1.27 patch for Ys I Complete, right? I install the needed codec for you, so it's odd that you would get this message if you used the latest patch. Only issue I could think of is if you downloaded one of those old ISOs that include my really old CAB-based patches.
EDIT: OK, there's another possibility. I only overwrite with the last freeware Indeo Codec (v5.11) if the DLL currently in the system folder is older and of course it's copied if it's not there at all. Try this: Goto your windows system folder (\WINDOWS\SYSTEM32 for NT/2k/XP or \WINDOWS\SYSTEM for 98/ME, etc.) and delete a file name ir50_32.dll if it exists, then run either the Ys I v1.27 patch or the Ys II v1.00 patch. Either one will copy the free 5.11 version back.
I think what linked you to Ligos' site was caused by the newer DLL being present on an unexpected Windows version. Possibly. Anyhow, yeah, deleting ir50_32.dll from your SYSTEM folder if present and re-running any of the latest patches might solve the problem, so there's something to try.
Good luck.