Write null bytes in a file instead of correct strings

With the following considerations:

• In over a decade of programming python, I've never come across a compelling reason to use global. Pass arguments to functions instead.
• For ensuring files are closed when finished with, use the with statement.

Here's an (untested) attempt at refactoring your code for sanity, assumes that you have enough memory available to hold all of the lines under a particular identifier.

If you have null bytes in your result files after this refactoring then we have reasonable basis to proceed with debugging.

import os
import re
from contextlib import closing

def list_files_to_process(directory='results'):
  """
  Return a list of files from directory where the file extension is '.res',
  case insensitive.
  """
  results = []
  for filename in os.listdir(directory):
    filepath = os.path.join(directory,filename)
    if os.path.isfile(filepath) and filename.lower().endswith('.res'):
      results.append(filepath)
  return results

def group_lines(sequence):
  """
  Generator, process a sequence of lines, separated by a particular line.
  Yields batches of lines along with the id from the separator.
  """
  separator = re.compile('^A:(?P<id>\d+):$')
  batch = []
  batch_id = None
  for line in sequence:
    if not line: # Ignore blanks
      continue
    m = separator.match(line):
    if m is not None:
      if batch_id is not None or len(batch) > 0:
        yield (batch_id,batch)
      batch_id = m.group('id')
      batch = []
    else:
      batch.append(line)
  if batch_id is not None or len(batch) > 0:
    yield (batch_id,batch)

def filename_for_results(batch_id,result_directory):
  """
  Return an appropriate filename for a batch_id under the result directory
  """
  return os.path.join(result_directory,"results-%s.res" % (batch_id,))

def open_result_file(filename,header="source,rssi,lqi,packetId,run,counter"):
  """
  Return an open file object in append mode, having appended a header if 
  filename doesn't exist or is empty
  """
  if os.path.exists(filename) and os.path.getsize(filename) > 0:
    # No need to write header
    return open(filename,'a')
  else:
    f = open(filename,'a')
    f.write(header + '\n')
    return f

def process_file(filename,result_directory='results/processed'):
  """
  Open filename and process it's contents. Uses group_lines() to group
  lines into different files based upon specific line acting as a
  content separator.
  """
  error_filename = filename_for_results('error',result_directory)
  with open(filename,'r') as in_file, open(error_filename,'w') as error_out:
    for batch_id, lines in group_lines(in_file):
      if len(lines) == 0:
        error_out.write("Received batch %r with 0 lines" % (batch_id,))
        continue
      out_filename = filename_for_results(batch_id,result_directory)
      with closing(open_result_file(out_filename)) as out_file:
        for line in lines:
          if line.startswith('L') and line.endswith('E') and line.count(',') == 5:
            line = line.lstrip('L').rstrip('E')
            out_file.write(line + '\n')
          else:
            error_out.write("Unknown line, batch=%r: %r\n" %(batch_id,line))

if __name__ == '__main__':
  files = list_files_to_process()
  for filename in files:
    print "Processing %s" % (filename,)
    process_file(filename)