The reason why you are getting the message is that the CPU load is not constant across different audio callbacks:
[env~] has a default analysis size of 1024. Depending on how it is implemented, this may (and probably does) mean that when running with blocksizes smaller than 1024, most of the time the object is doing nothing, simply collecting samples and storing them in a buffer. Then, when the buffer is full, it is analyzed all in one go. Now, the average CPU load (which is the one you see in the IDE) is low, because most of the time the object is doing nothing. But when it does the analysis, then it overruns the time available in the audio callback, thus causing the dropout message you see (and also causing a glitch in the audio output!). You can disable the warning by commenting out the relevant lines in
core/PRU.cpp, however that is not going to fix your audio glitch!
I think you cold re-implement
[env~] using a Pd abstraction that makes the CPU load constant (e.g.: do the processing as the samples come in, instead of waiting for the whole buffer to be filled), but I'd need to have a look at its C code to see what it does exactly.