Here's I would approach your problem:
filecontent = fileread('C:\path\to\yourfile.txt'); %read all file at once
filelines = strsplit(filecontent, {'\r', '\n'}); %split into line
isvalidline = ~cellfun(@isempty, regexp(filelines, '^\d{2}:\d{2}:\d{2}\.\d,\d{1,2}/\d{1,2}/\d{4},\d+,\d+,\d+(\.\d+)?N, \d+(\.\d+)?W,\d+(\.\d+),-?\d+(\.\d+)?,\d+,\d+(\.\d+)?$', 'once'));
C = textscan(strjoin(filelines(isvalidline), '\n'), '%q %{dd/mm/yyyy}D %f %f %s %s %f %f %f %7f', 'delimiter', ',')
The regular expression is rather long and I've made some assumptions based on the sample you've provided (e.g. most values are actually positive integers). The regular expression could be made to match exactly your textscan string but it would get even longer.
Here the regular expression is only used to validate a line, but you could use it to actually extract the values (as strings that would then have to be converted to the relevant type) and avoid the textscan altogether.
