Server 3.1 and Profile Manager woes

I was hoping the 3.1 upgrade would resolve the Profile Manager not working with "real" Code Signing certificates, but it seems to have made things even worse. (I swear there's no Q/A on this product.)
I readded my Digicert code signing certificate after upgrading (they have been amazing and have even issued me a special certificate to match all of the extensions and critical flags that the self-signed one Apple generates has).
With 3.1, it lets me pick the Digicert certificate for Profile Manager, but silently doesn't actually honour the preference. The self-signed certificate continues to be used. The logs are full of errors that I believe are related:
scep_helper.log after picking the certificate:
0:: [738] [2014/03/18 10:39:44.942] EXCEPTION:  Error <NSData *ExportIdentityToPKCS12Data(SecIdentityRef, NSString *__strong) (/SourceCache/RemoteDeviceManagement/RemoteDeviceManagement-864.18/Compiled/Fra mework-Base/Support/CryptoUtilities.m:483): "'((SecItemExport((__bridge CFTypeRef)items, kSecFormatPKCS12, 0, &keyParams, &pkcs12Data)))' error -25308">
0:: [738] [2014/03/18 10:39:44.943] SCEPHELPERS_GetIdentity: Caught exception NSData *ExportIdentityToPKCS12Data(SecIdentityRef, NSString *__strong) (/SourceCache/RemoteDeviceManagement/RemoteDeviceManagement-864.18/Compiled/Fra mework-Base/Support/CryptoUtilities.m:483): "'((SecItemExport((__bridge CFTypeRef)items, kSecFormatPKCS12, 0, &keyParams, &pkcs12Data)))' error -25308"
2014-03-18 10:34:41.330 AM sandboxd[442]: ([67306]) xscertd(67306) deny file-read-metadata /Library/Preferences/com.apple.security.plist
2014-03-18 10:34:41.352 AM sandboxd[442]: ([67306]) xscertd(67306) deny file-read-data /Library/Preferences/com.apple.security.plist
2014-03-18 10:36:04.224 AM servermgrd[148]: servermgr_certs[148] -[CertsRequestHandler(HelperAdditions) certificateForIdentity:]:  SecIdentityCopyCertificate (err = -25304)
And every 4 seconds:
2014-03-18 10:30:36.155 AM devicemgrd[210]:  SecOSStatusWith error:[-25291] The operation couldn’t be completed. (com.apple.security.xpc error 3 - <connection: 0x7fd3ed309e40> { name = com.apple.securityd.xpc, listener = false, pid = 0, euid = 4294967295, egid = 4294967295, asid = 4294967295 }: Connection invalid)
*sighs*

The private key already had the "Allow all applications to access this item". I went in there and hit Save anyway, and tried again. Still the same issue. Profile Manager lets me pick the certificate, but if leave the Profile Manager section and go back in, I find that it has been reverted.
And interestingly enough, if I set the values from the command line:
serveradmin settings devicemgr devicemgr:devicemgr:CodeSigningPrivateKey = /etc/certificates/Coverall\ Crew\ Corporation.5504F8C4DA768FC0253A9E8264EDAFC29AC75328.key.pem
serveradmin settings devicemgr devicemgr:CodeSigningCertificate = /etc/certificates/Coverall\ Crew\ Corporation.5504F8C4DA768FC0253A9E8264EDAFC29AC75328.cert.pem
serveradmin settings devicemgr devicemgr:CodeSigningAuthorityChain = /etc/certificates/Coverall\ Crew\ Corporation.5504F8C4DA768FC0253A9E8264EDAFC29AC75328.chain.pem
It's as if it completely ignores any updates.
I guess I may have to contact Apple for support.

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