Same problem here using the Entrust L1C chain. Works fine with Network Connect, etc., but not Pulse. I opened a case with JTAC. The first response I got was "try installing the intermediate CA (certificate) locally on the machine." I replied that deploying the chain to thousands of devices was not an option. I'll post again when I hear something useful.
Looks like this issue will be resolved in 7.1. Here's the response from JTAC:
"I would like to let you know this issue was replicated in the lab and it is fixed in 7.1.Rx. When you test using a web browser (Firefox, safari, internet explorer) on different platforms, you don't have this issue. I was able to confirm that this is a know issue reported with Pulse Client Ver. 1.0 and it is fixed from Pulse Client Ver. 2.0 (IVE OS 7.1Rx). Currently we donot have any ETA of when IVE OS 7.1Rx is expected to get released. Please use the following WORKAROUND to fix the issue for time being:
1. Open Internet Explorer and click Tools > Internet Options > Content tab > Certificates
2. Copy the intermediate CA certificate (attached to the email - rename the file from .txt to .cer) and install within IE (click Import under Intermediate Certification Authorities).
3. Once imported, try accessing the website again with Junos Pulse client. The error message will no longer appear."