[Nexus 5 Android Development] chairshot215:
Can confirm that it has not flashed the stock recovery with a multitude of flashing so is very very strange it happened as it is not even included in the zip. Have noticed with last few TWRP releases that sometimes after flashing a ROM SuperSU & Gapps that after booting either SuperSU or Gapps has not been installed. Found a fix in that after flashing Rom can reboot recovery and flash either Gapps or SuperSU. After will again reboot recovery and flash either SuperSU or Gapps depending on what I flashed after the first reboot recovery and has worked every time. If you have not done a full wipe you will still see the SuperSU app listed but is from a Play Store update installed on the data partition and does not have permission to install su binary on the system partition essentially braking root. If you flash the SuperSU zip in recovery will give you root again and because you have root will be asked to update the su binary from the Play Store update on the data partition. In short just flash SuperSU in recovery and you will be fine. Looking at screen shots thinking it was the Kohl's Store locater giving you the prompt for turning on location settings. Is just a guess but installed and when testing it does actually find the location and the prompt to turn on location settings disappears once the device finds your location. Overall would not actually call the first ip6 issue a bug in the Rom as the apps will need to update for the changes when they are added via future release. Still at this point unless the app devs are looking out for future changes in coming updates like for example not being able to access location at all with the added ip6 local-host. Still though not at that point so will look further but as one of the project manager stated on the work dev team from these bugs only effecting certain applications is more of a lazy programming on the app development than a Rom bug. Especially with apps like Kohl's who have the resource to have ip6 rules in place for these situations but are waiting until it first becomes an issue as apposed to being preemptive. Still though does not explain why you would receive a pop-up claiming location settings are off until the app finds the location. Otherwise during a conference call today at work downloaded a fresh copy of r4 and flashed by first doing a wipe of system and cache and installing the Rom and my Starship Kernel, rebooted recovery and flashed gapps. Once again rebooted recovery and flashed the superSU zip and then rebooted system. All was well after with no loss of root or TWRP. Was aware stock recovery was not flashed after rebooting recovery the first of two times. Can understand how would loose SU binary after flash as is actually expected. Again will still see SuperSU in the app list but is not installed as a system app so does not have permissions for installing SU binary. Needs to be a system app to do so. Looking into why Kohl's app showed location settings are not turned on but like I said in testing at least the store locater it does actually bring up a map with nearby stores listed so does actually work. It just shows location settings pop up with cancel and turn on location options that goes away after the app finds the devices location,

Thanks though as does not seem to be an issue with most apps. Could list a dozen or so that work perfectly fine and so far had one issue with transparent weather widget not working until removing the update for ip6 host and now again guessing Kohl's. Will let you know once is resulved.

Not sure what to say about the stock recovery being replaced as I jumped all over that one after reading and not able to reproduce. Even the updater-script makes no mention of recovery when the Rom is installed and like mentioned is not in the actual update.zip.