Brogsie,
No danger that I can think of. Now if the burner starts turning on and off rapidly you should turn it off and call a dealer because its hard on the burner. From looking on the Travis website I see that it uses the SIT 820 valve and pilot. I'm pretty familiar with that valve.
Here is a link to the manual although I'm guessing you have one.
(broken link removed to http://www.lopistoves.com/TravisDocs/100-01142.pdf)
If you want to rule out the switch you could always make a jumper with 1/4" female connectors and plug them into the valve. You'll plug them into the "TH" and "TPTH" leads on the valve. See page 17 of the manual for a picture of what I am talking about.
Also note the pilot and what it should look like on page 26. I'd confirm that the thermopile (left side of the pilot) has a good flame going to it. The thermopile is what powers (opens) gas to the main burner, while the smaller thermocouple keeps the pilot burning. If you need to turn the pilot up, you can adjust it by turning a screw on the valve.
Since your unit is brand new I really doubt it's a bad thermocouple, and your vent configuration looks like it would produce plenty of draft. IMO one of 2 things is happening, air is blowing the flame off of the thermopile, or the flame on the left side of the pilot is going out intermittently. So its either getting too much air, or not enough.
Some things I would try:
- When the stove acts up, see if you can view the pilot flame. If so is it lifting off of the thermopile? Does it look hyper/over active?
- If you have metal tape or even tin foil you can make a shield on the left side of the pilot to block air coming from the left side of the firebox. Block the path between the back of the firebox and the back of the log from the base of the pilot to about 1" above the thermopile.
One of 2 things will happen with the pilot shield, it will either solve the problem, or it will get Way worse. If it gets worse then I'd try opening the flue restrictor to allow more air into the firebox. If the shield solves the problem, you can leave it be, or try closing the restrictor more slowing the air flow into the firebox.
I hope this helps, you can always try calling the mfg and ask for their tech support guys. I'm willing to bet they have a pilot shield for your unit. Maybe some of the other guys on here have suggestions too?
Here is a link to a similar problem on another thread although his was much more obvious IMO.
https://www.hearth.com/talk/threads/28858/