I did some more digging on the yamaha website and was able to compare the 2 models side by side. It looks like the only difference is the receiver. The YHT-397 uses the HTR-3065, while the YHT-399U uses the HTR-3066. The differences between these 2 are as follows (from http://faq.yamaha.com/us/en/article/audio-visual/av-receivers-amps/rx/rx-v373_black_u/10254/7646/
The RX-V375/HTR-3066 is the latest model in that series and
has the following differences over the RX-V373/HTR-3065:
1. Discrete amp configuration
2. Low jitter PLL circuitry helps optimize sound imaging
Power and Demensions are identical.
Rated Output Power (8 ohms, 1 kHz, 0.9 % THD, 2 ch driven) 85 W + 85 W
Dimensions (W x H x D) 17-1/8" x 6" x 12-3/8"
Note on Weight:
Do to improved manufacturing processes, material upgrades, etc. They shaved a few ounces off the weight. Nothing more.