I've encountered several problems using large arrays with Arduino (V14,15 and 16 under Ubuntu). I'm trying to generate arbitrary waveforms from a DAC, the code works great if the waveforms are 256 bytes long, but when they are around 800 bytes long bad values are produced. Downloading similar code with a 3000 byte array bricks the Arduino by overwriting the bootloader. I tried putting line breaks within the data but that did not change the behavior. No errors show up when compiling any of this code.
An example of the problem code is here: http://www.solorb.com/elect/musiccirc/ArduinoLFO/ as DAC3.pde