First, if you're running 3.3.8 then you don't need to upgrade to recognize any of those three items. I assume by Trigger you refer to the open/close switch p/n 2843-222, that's the new part number for the old Triggerlinc p/n 2421. All three - the switch, the dimmers and the keypads work fine for me and I'm at 3.3.8. That was the latest version until this past Monday, and 3.3.9 includes very minor bug fixes.
Second, how are you accessing the ISY? If you're using the Java applet, then you need to make sure it's software rev matches the firmware on your ISY. From the task list on the top bar of your admin console, select "Help" --> "About" and a dialog pops up that shows your current ISY rev and UI rev. If these don't match you're in for problems.
Third, are you connecting your PC via
secure http? I've had all sorts of pain using the non-secure http port. Make sure you use the address https

IP address) for access. If you are using the Java applet, then the "finder" that pops up when you first start the app will automatically find the non-secure port - you need to use the add button to include the secure port in the list. Select the https: port every time you start up the app.
Next question, are all of your keypads and switches/dimmers dual band or are they all powerline only? I'm trying to figure out how robust your RF network is. I should point out that if you have all dual band devices (except, of course, the triggers which are RF only). There's really very little need for access points. Main reason for access points is for the PLM communications to bridge phases - a good number of installed dual band devices will do that anyway.
So ... once we've established some answers to my above questions, I see your struggle as two separate problems.
1) Why won't the wired devices (keypads, switches, dimmers) come into the ISY using the auto-linking process?
2) Why won't the open/close triggers link into the ISY without linking to another device?
The answer to #1 is likely to be found in either one of the setup questions above, or it is procedural. The steps are pretty simple. With the ISY admin console up and running (using secure port, correct Java console rev), you simple select "Link Management" --> "Start Linking". A dialog pops up that gives you three choices. I
strongly recommend choosing the default (remove existing links). This will clear out all links existing in any devices you add. (more on that later). Then you walk over to whatever device you want to link and push and hold the little "set" button just below the switch, until you hear it beep (about 3 seconds). As long as the new device has a communication path to the ISY, it will appear in a list that builds up at the bottom of the linking dialog on the admin console. You'll just see the Insteon address, but later you get the chance to rename it. You can add as many devices as you want, but keep in mind you need to keep track of the addresses so you can name them and do the setup correctly. When this is all done, just hit the "finish" button and you're on your way.
For the open/close - well, I've never managed to get the ISY to find these devices using the auto linking tool. I did struggle a bit getting the first one to work but using the manual add - "Link Management" --> "Add new Insteon Device" - works every time. However, with this method, you have to enter the Insteon address manually, along with the name you wish to use and the Device Type. I've had no success using auto discover to get the ISY to find the device type, so I just use the drop-down menu and select the correct type. Works like a charm. Of course, this switch is RF only, so it won't work if you're not in range of another Insteon wireless or dual-band device.
Now, getting to that "remove existing links" selection. I recommend you avoid setting up ANY links in Insteon devices other than through the ISY. If you manually link devices using the set buttons or some other method outside of the ISY, then the ISY will have no knowledge of these links and unpredictable things can happen. If you do the linking via ISY, it sends the link to the device(s) and keeps a record of that link in its own database. Once the actual device links and the ISY database mismatch, commands can be sent from a controller and the ISY may not track it. Hence, the recommendation when first linking to the ISY to remove existing links. If you are adding a device that was previously used in another location, old links could be residing in the device's table and that will eventually mess you up!!