Something that has helped us with general troubleshooting is having two reference systems. One application on Windows / IIS using Windows Authentication (no SiteMinder) and another that is protected with SiteMinder. This way, if you go to the standard non-SM one and it also doesn't work then can narrow in on client or browser configs / domain; once that is working then retry SM with the same setup.
Hopefully not muddying the waters too much, but just doing a bit of looking on my break, are all things set properly? One that was mentioned that I'm not too familiar with is this one:
--auth-schemes="digest,ntlm,negotiate"
Looking at Firefox, with v30 NTLMv2 is not supported for non-Windows platforms and NTLMv1 requires an extra setting - https://developer.mozilla.org/en-US/Firefox/Releases/30/Site_Compatibility#Security"
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If you encounter any problems on Firefox 30 or later, you can manually enable NTLMv1 using a preference. Note that NTLMv2 is not supported on non-Windows platforms, so OS X and Linux users have to toggle the preference to continue using NTLMv1 as below, though the NTLM auth support on non-Windows platforms is considered deprecated.
How to enable NTLMv1: type about:config in the location bar, click the "I'll be careful" button, findnetwork.negotiate-auth.allow-insecure-ntlm-v1, double-click on it to change the value to true.
Another workaroud here is using Firefox 24 ESR that still enables the NTLMv1 auth."
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Haven't looked through Chrome's notes to see if they have any gotchas for NTLM support on non-Windows, but probably worth a look. A lot of this stuff ends up being client/browser support more so than SM specific.
Really though if you want to maintain current with security updates and supported capabilities, going Kerberos is probably worth a look. Doesn't necessarily answer your NTLM problem, but for authentication it's much better.