[ossiblue]

After rereading this thread, I'm leaning toward an ignition problem. The warm start problem is typically associated with a residual pressure loss but in your case, it starts when more time passes and that doesn't make sense as residual pressure will not increase over time. Additionally, your test using the plunger did not alleviate the problem. Tony's question about the CDI is worth an answer as well.

Just throwing it out there because I have no experience with later CIS, but can a faulty frequency valve or electrical connection related to it cause a problem like this?