N.G. Fireplace - Pilot noisy, fluttering and going out.

Hi all! I'm new here, so excuse me if I come off as a complete boob. I have a HeatNGlo direct vent gas fireplace with a pilot problem. Its strong and smooth with the glass removed, but shudders and is noisy with the glass on. Usually, goes out within an hour or two. I recently replaced the entire pilot assembly (thermocouple, thermopile, ignitor) because the original ignitor was fried and the pilot was orange and smoking up the logs / glass and no amount of cleaning the orifice would improve it. After installing the new assembly, the pilot is strong, quiet and blue as it should be. Once I reinstall the glass, it gets noisy and flutters before going out. All was well before, but I checked the venting just to be sure and its clear on both the inner and outer tubes. Its worked fine for 15 years, but I just felt these parts were due for replacement and they're the correct parts for the unit. Anyone have any ideas? Whats changed to cause this? Thanks in advance Barney.

HeatNglow - model SL36GDV. Horizontal vent. Nothing has changed in the 15 years since installation and the vent is clear. The only change was a new pilot assembly that resolved several other problems.....ie. toasted ignitor, worn/blocked pilot orifice etc. Appears to be perfect again, but this new problem has surfaced. Thanks for your help!

Identical except the hole for mounting it is a side mount versus top. I simply bent it flat again and its perfect. The package it came in had a factory type sticker with bar code and said SL36GDV. Plus I bought it from a reputable fireplace/heating parts supplier......not some chinese website. Like I said it works perfectly otherwise. I'm wondering if there is an "air shutter" or some other adjustment for the air ratio of the pilot that I've overlooked?

Hey Bob....thanks for the speedy reply. I thought there may be an air shutter on the pilot, but you're right, there is only one for the main burner and I left it alone since its been the right setting since new and because my problem lies within the pilot system. I took it all apart again today to double check my work and noticed that I had bent a small sheet metal tab on the left side of the pilot bay, to enable "dropping in" the new assembly. Thinking it was nothing (and it may well be....time will tell) I never bent it back, but I did today. Its running fine.......so far. Hopefully this message doesn't jinx everything If this isn't the problem, then I'm gonna take up drinking again........grin. Thanks for your input....Cheers! Off to fix the dishwasher now......not draining completely.......ugh! If I have time after that, I have to deal with a wasp problem under my eaves......the fun never ends!