Couple possibilities on the bags:
1) The bags at max size would be partially offscreen, so are being automatically moved fully on screen before being resized down to fit their slot count. This would be more likely if you're using a vertical bag placed near the bottom of the screen, but could happen with any bag placed near screen bottom. Try checking the Game Options "Allows windows off screen" button. You may HAVE to move your bags farther from screen bottom.
2) For some reason those windows aren't being saved by SOE. There's absolutely no difference UI wise between a Bank bag, House bag, or Inventory bag, so if some are saving, that tells me the bag file is working as intended.
3) You're using an old bag file not included with the latest download that doesn't have the Stay-put feature and are just lucky some bags are staying put
If you're not using a stay-put bag, bags whose custom location were never saved to the server will persist in always using default positioning.
Regarding Inventory states on log-in... not surprised. The UI is unaware of custom windows during initial load, so it doesn't know where the Dock is untill after its resized the inventory and finished loading the world. Should only be an issue if Inventory is saved as visible when you last logged out.