Welcome to the forum.
Just to make sure that I am on the same page, as you, when you say "render," you are speaking of hitting the Enter/Return key, to Render the Timeline, for the smoothest playback. Is that correct?
Now, on your Timeline, when you make a changes, such as adding an Effect, or any sort of overlay, such as a Transition, PiP, or an overlay Title, you will get a red line above that Clip, or portion of a Clip. If one hits the Enter/Return key, ONLY that/those section(s) with the red lines, will Render. However, if I read correctly, you are getting the red lines, BUT not all of that/those Clip(s) will Render. Is that correct?
When only part of a Timeline Renders, the first two things to check are the position/length of the WAB (Work Area Bar). That can become accidentally set to too small a portion of the Timeline. The easiest way to make sure that the WAB has been extended to the full Timeline is to hit the \ (Backslash key), to zoom out to see the full Timeline, and then find the little "box" in the middle of the WAB. Dbl-click on that, to make sure that it has expanded to cover 100% of the Timeline.
The next thing to check, is has an In, or Out Point been set on the Timeline. This can happen accidentally, if the CTI (Current Time Indicator) has been set to some point other than 00;00;00;00, or the full Duration of the Timeline, and the I (eye key) for In Point, or the O (oh key) for Out Point has been hit. The way to look for an In Point, or Out Point on the Timeline, is to look at the Time Ruler, and see if it is a different shade of gray, over Clips, before the end of the Timeline.
If neither the WAB, or a Timeline In/Out Point has gotten set, I have a question: where are the Scratch Disks for that Project set? Especially with external HDD's, I have that location set to "Same as Project," so that all Render files, and the Media Cache, etc., are set to that same HDD.
How much defragmented free-space do you have on the HDD, where the Scratch Disks are set?
If to the external HDD, what is its connection type, i.e. eSATA, FW-400/800, USB, etc.?
For the OS, how much defragmented free-space exists on your C:\?