I need to control a large matrix of arduino neopixel strips--ultimately, thousands, but currently a strip of 960 pixels. However the limit seems to be at 622 pixels--any higher than that, and the data stream seems to stop. What could be causing this and how can i get around it?
LarryD is undoubtedly correct, you hit the RAM limit on the Uno.
There are many choices these days to upgrade from Uno, such as Mega, Due, Teensy 3...
Tell us more about your application and we can recommend one. For example would WiFi access be useful? The ESP8266 chips can control neopixels and be programmed with the Arduino IDE.