Yes, I've encountered this same problem. It is quite frustrating considering the price of the FFG expansions and the important role banners play in the game. As such an important element, you'd think FFG would develop a quality gamepiece. I bought Horiffic Hoardes and I placed the banner stickers the same day I got the expansion. I played a game using Horiffic Hoardes that weekend, and most of the stickers were peeling off. I had to put the game aside to glue the banners into place. I have a BattleLore basic set and Scottish Wars Expansion when they were produced by Days of Wonder, and this was never an issue with the Days of Wonder products I puschased. I am also pleased with my customer service experience with FFG. However, I think they may be starting to produce a sub-standard product in terms of game pieces in the interests of cost cutting.
As to glueing the banners...I used simple crazy glue (sometimes referred to as super glue). I used the small, triangle shaped bottle with the thin head where the glue comes out. I just peeled the banner back a bit and I placed the glue onto the plastic standard piece. I then used a toothpick to push the banner back down onto the plastic. Sometimes when you push the banner onto the glue, some glue may seep around the side depending on how much glue you put on the plastic. This is no big deal because once the glue dries, it is transparent and you don't notice it. However, if you touch this during the drying process, you will find the banner stuck to your hand, and this can mess-up your banner when you remove it. Therefore, be very careful when glueing the banners in this way. This is why I used a toothpick.
I would hope FFG would release banner packs for BattleLore like they did for Battles of Westeros, but I don't think this is likely. Someone on these forums (in another thread) mentioned making you own stickers. I know you can buy sticker sheets for your printer, but does anyone know of a template or something where you can print out stickers in the shape and size of the BattleLore standards and pennants?