Bugsie, if it's not the patch messing you up, the most common mistakes I've seen people make with the mod manager are 1) merging mods into the official patch folder instead of a separate folder one in the update folder 2) not creating a folder to put the merged mods in. The official instructions are kind of confusing because the guy who wrote them is a coder, not someone who focuses on that stuff, hehe, but your work flow should be:
Create a folder called something like "Active Mods" (away from your dragon age folder) to put your mods in.
Create a folder inside the DA:I update folder called "merged" (you can call it whatever you want but modders will refer to it as your Merged folder)
Run the mod manager and navigate to "active mods", make sure the mods you want are selected, then merge to your Merged folder
if you're doing all that and it still won't work, then I would be happy to help you troubleshoot more, you can PM me anytime