It sounds like you're clips have timecode breaks during your Capture Now process in Final Cut Pro. The reason you are losing around 3 seconds of footage in each "subclip" is due to the fact that Final Cut Pro felt that that the section of time that was missing was also missing timecode and so it skipped capturing that part of the clip during the Capture Now process.
Unfortunately, nothing can really fix broken timecode successfully, but there are ways to get Final Cut Pro to capture the entire clip without making subclips and to possibly get your lost section of time back between subclips too. If you go to "User Preference" and then the "General" tab, you'll see a number of check boxes. On the right side of the "General" tab window you'll see a drop down window that says "On timecode break:" I suspect you'll see the "Make New Clip" option selected by default. In order to get Final Cut Pro to stop making new clips every time it encounters a timecode break, make sure to choose the "Warn After Capture" option on that drop down menu. If my suspicions are right, that should do the trick!