Why would fgets skip data?

I'm working on this code to read in an array of integers from a file, and I have it working for one test file, but I added another line to the array and for some reason when it has to read this extra line, fgets() seemingly "skips" over a few characters.

Attached is the function. This is the output I've been getting (the last line of the file, no different than any other line, has the numbers 5, 2, and 1. As shown by the sample output, doing a manual scan of the char *line that I read in shows that it somehow read in the 1 and a \n but "skipped" the first few characters...

Rows: 4
Cols: 3
Allocating 48 bytes for array...
'12     5       7
¿'
'12     5       7
'
'12'    Putting 12 in [(0 * 3 + 0) *4] = [0]
'5'     Putting 5 in [(0 * 3 + 1) *4] = [4]
'7'     Putting 7 in [(0 * 3 + 2) *4] = [8]
'8      16      2
¿'
'8      16      2
'
'8'     Putting 8 in [(1 * 3 + 0) *4] = [12]
'16'    Putting 16 in [(1 * 3 + 1) *4] = [16]
'2'     Putting 2 in [(1 * 3 + 2) *4] = [20]
'3      9       18
¿'
'3      9       18
'
'3'     Putting 3 in [(2 * 3 + 0) *4] = [24]
'9'     Putting 9 in [(2 * 3 + 1) *4] = [28]
'18'    Putting 18 in [(2 * 3 + 2) *4] = [32]
'       1
¿'
''
Rows: 4
Cols: 3

/*
getArrayFromFile
-----------------------
char *filename - pointer to the name of the matrix file to open.
int *rRows - pointer to allocated space to store the number of rows
int *rCols - pointer to allocated space to store the number of columns
*/
int *getArrayFromFile(char *filename, int *rRows, int *rCols)
{
	int *rows = malloc(sizeof(int));
	int *cols = malloc(sizeof(int));
	
	getFileInformation(filename, rows, cols);
	
	printf("Rows: %d\n", *rows);		//DEBUG
	printf("Cols: %d\n", *cols);		//DEBUG
	
	int bytesToAllocate = ((*rows)*(*cols)*sizeof(int));
	printf("Allocating %d bytes for array...\n",bytesToAllocate);
	
	int *A = malloc(bytesToAllocate*2);
	// Not sure why I'm multiplying it by 2... it allocated half of what I wanted.
	
	// ================ FILL ARRAY WITH NUMBERS ================
	
	FILE *file;
	file = fopen(filename, "r");
	if(file == NULL)
	{
		fprintf(stderr,"File could not be opened.");
		exit(1);
	}
	
	char *line = malloc(sizeof(char)*255);
	int col = 0, row = 0;
	
	//fgets(line,255,file);
	//while(!feof(file))
	while(fgets(line,255,file) != NULL)
	{
		int q = 0;
		printf("'");
		for(q = 0; q < 255; q++)
		{
			printf("%c",line[q]);
		}
		printf("'\n");
		
		printf("'%s'\n",line);		//DEBUG
		int i = 0;
		while(line[i] != '\n' && line[i] != '\0')
		{
			// Skip white space until we hit a number.
			while(line[i] == ' ' || line[i] == '\t')
			{
				i++;
			}
			
			// Reset number collector
			int numCount = 0;
			char num[10] = {'\0','\0','\0','\0','\0','\0','\0','\0','\0','\0'};
			
			// Get number until we hit white space again.
			printf("'");	//DEBUG
			while(line[i] != ' ' && line[i] != '\t' && line[i] != '\n' && line != '\0')
			{
				printf("%c",line[i]);	//DEBUG
				num[numCount] = line[i];
				numCount++;
				i++;
			}
			printf("'\t");	//DEBUG
			
			int positionToPlace = (row * (*cols) + col)*sizeof(int);
			printf("Putting %d in [(%d * %d + %d) *%d] = [%d]\n",atoi(num),row,*cols,col,sizeof(int),positionToPlace);
			
			// We have number, put it in array
			A[positionToPlace] = atoi(num);

			col++;
			i++;
		}
		row++;
		col = 0; // Reset col in preparation for next row.
		
		//fgets(line,255,file);
	}
	
	free(line);
	fclose(file);
	
	// =========================================================
	
	*rRows = *rows;
	*rCols = *cols;
	
	free(rows);
	free(cols);
	
	return A;
}

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