New DVR Issues (First Run, Channel Switching, etc.)

Question

I've spent the last 30 minutes trying to find answers through the search with no luck, so sorry if I missed something.
I recently switched to FIOS from RCN cable in New York.  I've gone through trying to setup my DVR and am running into issues and was hoping for some answers.
1.  I setup two programs to record at 8PM, I was watching another channel at the time and only half paying attention.  Around 8:02 I noticed a message had popped up asking if I would like to switch channels to start recording.  I was expecting it to force it to switch like my old DVR, but in this case it didn't switch and I missed the first two minutes of one of the shows.  I typically leave my DVR on all day and just turn off the TV, this dual show handling will cause issues with that if I forget to turn off the DVR.  Is there a setting I can change that will force the DVR to choose one of the recording channels?
2.  I setup all my recordings for "First Run" because I only want to see the new episodes.  One show I setup was The Daily Show on comedy central, which is shown weeknights at 11pm and repeated 3-4 times throughout the day.  My scheduled recordings is showing all these as planned recordings even though only the 11pm show is really "new".  Most of the shows I've setup are once a week so they aren't a problem, but this seems like it will quickly fill my DVR.  Any fixes?
Thanks for the help.
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Answer 1

I came from RCN about a year ago.  Fios is different in several ways, not all of them desirable.  Here are several ways to get--and fix--unwanted recordings from a series recording setup.
Some general principles. 
Saving changes.  When you originally create a series with options, or if you go back to edit the options for an existing series, You MUST save the Series Options changes.  Pretty much everywhere else in the user interface, when you change an option, the change takes effect immediately--but not in Series Options.  Look at the Series Options window.  Look at the far right side.  There is a vertical "Save" bar, which you must navigate to and click OK on to actually save your changes.  Exiting the Series Options window without having first saved your changes loses all your attempted changes--immediately.
Default Series Options.  This is accessed  from [Menu]--DVR--Settings--Default Series Options.  This will bring up the series options that will automatically be applied to the creation of a NEW series. The options for every previously created series will not be affected by a subsequent modification of the Default Series Options.  You should set these options to the way you would like them to be for the majority of series recordings that you are likely to create.  Be sure to SAVE your changes.  This is what you will get when you select "Create Series Recording" from the Guide.  When creating a new series recording where you think that you may want options different from the default, select "Create Series with Options" instead.  Series Options can always be changed for any individual series set up later--but not for all series at once.
Non-series recordings.  With Fios you have no directly available options for these.  With RCN and most other DVRs, you can change the start and end times for individual episodes, including individual episodes that are also in a series.  With Fios, your workarounds are to create a series with options for a single program, then delete the series later;  change the series options if the program is already in a series, then undo the changes you made to the series options later; or schedule recordings of the preceding and/or following shows as needed.
And now, to the unwanted repeats. 
First, make sure your series options for the specific series in question--and not just the series default options--include "First Run Only".  If not, fix that and SAVE.  Then check you results by viewing the current options using the Series Manager app under the DVR menu.
Second, and most annoying, the Guide can have repeat programs on your channel tagged as "New".  It happens.  Set the series option "Air Time" to "Selected Time".  To make this work correctly, you must have set up the original series recording after selecting the program in the Guide at the exact time of a first run showing (11pm, in your case), and not on a repeat entry in the Guide.  Then, even it The Daily Show is tagged as New for repeat showings, these will be ignored. 
Third, another channel may air reruns of the program in your series recording, and the first showing of a rerun episode on the other channel may be tagged as "New".  These can be ignored in your series if you set the series option "Channel" to "Selected Channel".  Related to this, if there is both an SD and HD channel broadcasting you series program, you will record them both if the series option "Duplicates" is set to "Yes".  However, when the Channel option is set to "Selected Channel", the Duplicates Option is always effectively "No", regardless of what shows up on the options screen.  
As for you missing two minutes,  I have sereral instances in which two programs start recording at the same time.  To the best of my recollection, whenever the warning message has appeared, ignoring it has not caused a loss of recording time.  You might have an older software version.  Newest is v.1.8.  Look at Menu--Settings--System Info.  Or, I might not have noticed the loss of minutes.  I regularly see up to a minute of previous programming at the start of a recording, or a few missing seconds at the beginning or end of a recording.  There are a lot of possibilities for that, but the DVR clock being incorrect is not one of them.  With RCN, the DVR clocks occasionally drifted off by as much as a minute and a half.