Hi MadMike,
Sorry you're having problems with your TubePress install.
When I look at the debug output, here is what I see:
[2013-05-12 06:57:03] [DEBUG] Shortcode Parser: Candidate options detected in shortcode: [tubepress thumbHeight='105' thumbWidth='135']
[2013-05-12 06:57:03] [DEBUG] Shortcode Parser: Name-value pair detected: thumbHeight = "105" (unfiltered)
[2013-05-12 06:57:03] [DEBUG] Shortcode Parser: Name-value pair detected: thumbHeight = "105" (filtered)
[2013-05-12 06:57:03] [DEBUG] Shortcode Parser: Name-value pair detected: thumbWidth = "135" (unfiltered)
[2013-05-12 06:57:03] [DEBUG] Shortcode Parser: Name-value pair detected: thumbWidth = "135" (filtered)
[2013-05-12 06:57:03] [DEBUG] Memory Execution Context: Accepted valid value: thumbHeight = 105
[2013-05-12 06:57:03] [DEBUG] Memory Execution Context: Accepted valid value: thumbWidth = 135
[2013-05-12 06:57:03] [DEBUG] Memory Execution Context: Accepted valid value: resultsPerPage = 3
[2013-05-12 06:57:03] [DEBUG] Memory Execution Context: Accepted valid value: views =
[2013-05-12 06:57:03] [DEBUG] Memory Execution Context: Accepted valid value: description = 1
[2013-05-12 06:57:03] [DEBUG] Memory Execution Context: Accepted valid value: descriptionLimit = 50
[2013-05-12 06:57:03] [DEBUG] Memory Execution Context: Accepted valid value: playerLocation = popup
[2013-05-12 06:57:03] [DEBUG] Memory Execution Context: Accepted valid value: thumbHeight = 105
[2013-05-12 06:57:03] [DEBUG] Memory Execution Context: Accepted valid value: thumbWidth = 135
[2013-05-12 06:57:03] [DEBUG] Memory Execution Context: Accepted valid value: paginationAbove =
[2013-05-12 06:57:03] [DEBUG] Memory Execution Context: Accepted valid value: paginationBelow =
[2013-05-12 06:57:03] [DEBUG] Memory Execution Context: Accepted valid value: theme = sidebar
[2013-05-12 06:57:03] [DEBUG] Memory Execution Context: Accepted valid value: fluidThumbs =
What this shows is that you have the following settings set for your TubePress:
Results Per Page = 3
Theme = Sidebar
Player Location = Popup
With this setting, you will not see the pagination (page numbers) because you are using the Sidebar theme. You will also only display 3 videos per your setting. Also, you are not seeing any video player at the top of the page because of your theme.
To resolve this, there are two different things you can do: One is easy, the other a little more involved.
1) (Easy way) You can remove TubePress from your WordPress installation completely and then reinstall and re-start configuration from default.
2) (More involved) Go through your TubePress settings tabs and make the changes within the settings (saving each tab) and set it up the way you want it to work.
Let us know if you have any other questions/problems.
Thanks!