FontExplorer X Pro corrupting system fonts (mainly Helvetica)

Yosemite, Clean Install
I recently installed a trial of FontExplorer X Pro because I thought it was about time I moved up to a professional font management tool. Shortly after installing it, and importing my fonts, things started to go haywire. As you can see below, Messages.app, websites (GoDaddy.com pictured) and Mail.app display a strange A-in-a-box character in place of what should be actual, legible copy. I have been trying to work with FontExplorer's tech support but they have been unhelpful so far, not to mention it takes them days to respond. I believe I've (so far) narrowed this down to HELVETICA and I'm sure it has something to do with Mac OS X now using Helvetica Neue throughout the System in place of what used to be Lucinda I believe
I'm just at a loss for what to do. I can't seem to get my system fonts back in order. I've tried uninstalling the software, and starting over, and nothing has helped. I can clear the Font Cache, restart, and then everything is fine...but as soon as I open a document with Helvetica Neue in it, everything else goes haywire again. Deactivating Helvetica Neue is not an option. I am a graphic designer, I need Helvetica for nearly everything.
I would appreciate any suggestions at all, thank you.
Messages.app: The timestamp is replace with these characters.
Safari/Godaddy.com: All the text in the login area are the same character.
Again, in Mail.app, this contact's signature is completely unreadable.

Anyone? No one from Linotype has been able to answer my questions either.
Like I said, the problem started after I upgraded from 10.6.6 to 10.6.8. The same issue occurs on 2 different computers both running 10.6.8, even though one of them is a fresh install.
I've tried resetting the FontBook by booting into Safe Mode, but even that doesn't fix it. However I'm now able to add metadata and create sets, but only for system fonts (i.e. anything with a lock icon).

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What Apple applications need the System fonts (Helvetica and Helvetica Neue) ?
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Message was edited by: macjack

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mount -uw /
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Is this very problematic
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Replacing a System Font

Hello,
We've been having some font issues and I think I'm close to clearing them up but have a question. We use FontAgent Pro and in that, we have a Helvetica font and a Helvetica Neue font. Both of which are also System fonts. I did the Restore Standard Fonts in Font Book. I've noticed that the System font versions of those fonts actually have less fonts in them than the versions in FontAgent Pro. (i.e. condensed black oblique, the whole thin family, etc...) So my question is can I replace the System Font versions with my FontAgent versions and if so, how do I do it without screwing up the system.
Thanks in advance,
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So you've got full Type 1 PostScript sets you'd prefer to use all the time. There are some problems with this, but not impossible to deal with.
You may find the information in my article Font Management in OS X useful. In the section on minimum required fonts for the various versions of OS X, I have this information on Lion, which also applies to 10.8 and 10.9.
Previously, you could remove Apple's Helvetica fonts and permanently use Type 1 PostScript versions in their place. Not any more. Address Book is one app which will not launch if Apple's version of Helvetica is missing. So for prepress, designers or others who must use Type 1 PostScript versions of Helvetica or Helvetica Neue, it is now a requirement to copy Apple's Helvetica fonts to a non Fonts folder location, remove them from the System and ProtectedFonts folders, and then set up separate sets in your font manager for Apple's Helvetica fonts, and another for your third party Helvetica fonts. Then turn on whichever set you need at the time and turn the other set off. It's not perfect as you may need the the Type 1 fonts open, which will leave you temporarily unable to open Address Book until you disable the Type 1 fonts and turn the Apple supplied versions back on. There is no way around it. You simply can't have both on at the same time.
Instructions for copying, and then removing the Apple supplied versions of Helvetica are noted in section 5. That's pretty much what you'll have to do in order to have access to your full set of T1 PS fonts.
I may receive some form of compensation, financial or otherwise, from my recommendation or link.

System fonts not showing in Font Book

I am using Font Agent Pro as a font manager and am wondering if there's a conflict with it and Apple's Font Book. I cannot get the system fonts to show up in Font Book and, hence, those (System) fonts don't show in Apple apps, e.g., Safari, Grapher, Text Edit, etc., etc.
The only way I can get the system fonts to show in apple apps it to drag the System>Library>Fonts folder to the "Collection" column onto the "Computer" collection. This is fine, but it copies the System fonts to the ComputerName>Library>Fonts folder.
I've tried for hours to get the System fonts to show in Font Book and do it without the System fonts being copied to the Library or User folder, i.e., I want the System fonts to stay in the System fonts folder only.
If I boot into another partition and bring up Font Book everything works as I would expect, and Font Agent Pro is not installed on that partition...
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Hi PS1,
I am using Font Agent Pro as a font manager and am wondering if there's a conflict with it and Apple's Font Book.
Yes, in a sense. If you always open and close your fonts through FAP's interface, then it's no problem leaving Font Book on your Mac. It will simply sit there and take up a small amount of disk space.
That said, it's still a nuisance having more than one font manager on your computer at a time. Say you disable all of the fonts in Font Book that you can. Assuming the fonts are still in the /Library/Fonts/ folder, you then turn them on and off with FAP. The problem then is which orders are the applications going to believe? Are the fonts active, according to FAP? Or inactive, according to Font Book?
Also, if you double click on any font to quick activate it, both FAP and Font Book will activate the font. So you will find yourself confused fairly often when you deactivate the font in FAP, but they still keep showing up in your applications as active. That would be because Font Book is still holding it open.
So if FAP is going to be your main font manager, then copy Font Book off to another disk for safe keeping (so you don't have to use Pacifist or an OS install to get it back on your system if you need, or want to), and then remove it from your hard drive.
Definitely don't remove the /System/Library/Fonts/ folder! If you remove Lucida Grande from its default location in any way, you will lose control of your desktop. The only way I can think that Taavi managed to accomplish this was moving files around booted to an external drive, or from another Mac via FireWire Target Mode. It's impossible to do on the same drive your booted to. You'll lose control of the desktop every time if you remove Lucida Grande. Although Taavi may have made his/her copy to the /Library/Fonts/ folder. That at least would still leave an active copy of Lucida Grande somewhere, but I highly recommend against that sort of handling of the system fonts.

FontExplorer X Pro corrupting system fonts (mainly Helvetica)

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