Having multiple ESPs is not an error, according to the EFI specification. That said,
Microsoft doesn't support such configurations. I know for a fact that the Windows 7 installer malfunctions when it's shown a disk with multiple ESPs. I don't know if Windows 8 suffers from the same bug, or if anything running within Windows would do so. Thus, I do generally agree with the advice to consolidate all your ESPs into one, although in the short term, it should be possible to continue using multiple ESPs.
GRUB, like the EFI itself, should be able to cope with multiple ESPs. Indeed, the fact that your custom entry worked verifies this in reality. Thus, there's a bug in the OS-probing scripts. (Other peoples' experience points to the same conclusion.) In the short term, it's probably best to just keep using your custom entry and ignore the ones that the buggy OS prober generates, or take other steps to remove the non-functional entries.
It's
imperative that you
disable Fast Startup in Windows when dual-booting. Leaving that feature active can result in an inability to access shared partitions (including the ESP) from Linux and/or in filesystem corruption. It's entirely possible that this feature is what's making it impossible to write to the disk's original ESP. Note that I'm talking about a
Windows feature. Many EFIs have a firmware feature with a similar name, and that feature is often OK to leave active. (It tends to take shortcuts in the system initialization, which are often OK but can sometimes make it harder to access the firmware setup utility or boot from external disks.) Disabling the firmware feature will
not disable the Windows feature.
Quite honestly, I have a low opinion of GRUB 2 because of its OS prober and other problems. This is one of the reasons I forked rEFIt into
rEFInd, which does a much better job of locating and running EFI boot programs than does GRUB. OTOH, setting up rEFInd with Secure Boot active can require some extra hoop-jumping. The
rEFInd Secure Boot documentation goes into this in detail. With any luck, though, if you just install the rEFInd RPM, it will be
mostly working -- you'll just need to add the rEFInd certificate file to your NVRAM when you reboot. OTOH, since you've gotten GRUB more-or-less working, leaving it in place may be an easier way to go for now. I mention rEFInd as an option in case you have further problems or if you simply dislike GRUB.