Ok solved it in a not very elegant way. I dont know why the /n wasnt being reconised in textscan but what I did was call text scan AGAIN on just that problem row and then it worked fine. I then added the row numbers and added the offset of blank rows:
fid = fopen('C:\Users\Rafa\Documents\Data\SonRMay172017Experiment\H17-1001-01_004_Subcutaneous SonR.txt', 'rt');
s = textscan(fid, '%s', 'delimiter', '\n');
ss=textscan(s{1,1}{17,1}, '%s', 'delimiter', '\n');
channel_title_row=17+length(ss{1,1})+1;
fclose(fid);