There could be a number of things that are preventing the web application from being created on the second server. Here are a few things you can check:
Timer Service: Nearly everything that is done on multiple farm servers is done through the SharePoint timer service. Make sure that is running on all servers in your farm. If it is running, it is possible that something is hung up. Restarting the timer service on each server in the farm can sometimes help with hung timer processes.
Patch Level: I've not heard of something like this happening when farm servers are on different patch levels, but you may want to verify that SharePoint is on the same patch level for each server in the farm.
ULS Logs: Anything and everything that is done in SharePoint will show up in the ULS tracing logs. Keep in mind that there are ULS logs located on each server in the farm, so if there is something specific happening in the timer service on the server that is failing to create the web application in IIS it will show up in the ULS logs on that server. You may need to increase the tracing level as high as 'Verbose' to get a detailed picture as to what is happening. The ULS logs will most often lead you in the direction you need to go to find the source of the problem.
Windows Event Logs: If there is something happening at the OS or IIS level, it is likely that there will be an entry in the Windows Event logs that can help point you in the right direction here too.
IIS is running: I would of course assume that the World Wide Web Publishing service is up and running on the server that is failing. If IIS is in a hung state, it may be necessary to restart this service or perform an 'iisreset' on that server.
Another item to verify is that the 'Microsoft SharePoint Foundation Web Application' role is running on that server in your farm. You can check this in Central Admin. It should be in a 'Started' state.
The above items should be good starting points for you to troubleshoot as to why the web application is not being created in IIS.