My code is buffering my output. I don't find this funny.

[cprogramnoob]

#define _CRT_SECURE_NO_WARNINGS
//#include <stdlib.h>                                                    // used by atoi and malloc
#include <stdio.h>                                                        // printf library
#include <string.h>                                                        // library manipulates strings.


char message_cache1[240];
char message_cache2[240];


int main() {
    FILE *fp;
    char filename[]="ABseeD002.txt";
    fp=fopen(filename, "w");
    if (fp == NULL) { printf("\n The file %s could not be opened.", filename); } //  if error occurs
    printf("Items will be initiated in the same DIRECTORY as this program. Enter EXIT on a BLANK line to exit.\n"); 
    printf("Please enter a message you desire to encode. Limited to 100 characters per line.\n:");                                                
    gets(message_cache1); //  gets message from keyboard
    while (!strstr(message_cache1, "EXIT")) {
        printf("\nlengthofcache1:%d\n", strlen(message_cache1));
        if ((strlen(message_cache1)) > 5) { 
            for (int i = 5; i < 240; i++) { 
                if (message_cache1[i]!=NULL) { message_cache2[i-5] = message_cache1[i];    }
            }
            printf("\nlengthofcache2:%d\n", strlen(message_cache2));
        }
        printf("\n%s\n", message_cache1);
        printf("\n%s\n", message_cache2);
        for  (int count=0; count <=4; count++) // review for loops maybe sing a song about them.
            {
                int ascii_cache=message_cache1[count];
                if (ascii_cache >= 32 && ascii_cache <= 99)     {    fprintf(fp, "0");                    } // dump the leading 0 to file.
                if (ascii_cache != 0)                            {    fprintf(fp, "%d", ascii_cache);        } // dump to file.    %d = integer    
            }
        fprintf(fp, "\n");
        strcpy(message_cache1, "");                        // message 1 empty
        printf("\nlengthofcache1:%d\n", strlen(message_cache1));
        printf(":%s", message_cache2);                    // prints message 2
        gets(message_cache1);                            // gets new message1
        printf("\nlengthofcache1:%d\n", strlen(message_cache1));
        strcat(message_cache2, message_cache1);            // adds message1 to message2
        strcpy(message_cache1, "");                        // message 1 empty
        //printf("\nMessage1:%s", strlen(message_cache1));
        //puts(message_cache1);
        strcpy(message_cache1, message_cache2);            // copies 1 to 2
        strcpy(message_cache2, "");                        // empties 2
        printf("\nlengthofcache1:%d\n", strlen(message_cache1));
        printf("\nlengthofcache2:%d\n", strlen(message_cache2));
        printf("\n%s\n", message_cache1);
        printf("\n%s\n", message_cache2);
    }
    fclose(fp);  // closes the cfile pointer 
    printf("Encoding....completed to the file %s.", filename);
    return 0;
}

INPUT 123456
OUTPUT:
049050051052053
054051052053

[Salem]

2022 and still using gets() - Ugh!!!!

gets has been dead for a decade.
gets, gets_s - cppreference.com

What are you expecting to see?

$ ./a.out 
Items will be initiated in the same DIRECTORY as this program. Enter EXIT on a BLANK line to exit.
Please enter a message you desire to encode. Limited to 100 characters per line.
:123456

lengthofcache1:6

lengthofcache2:1

123456

6

lengthofcache1:0
:6

lengthofcache1:0

lengthofcache1:1

lengthofcache2:0

6



lengthofcache1:1

6



lengthofcache1:0
:EXIT

lengthofcache1:4

lengthofcache1:4

lengthofcache2:0

EXIT


Encoding....completed to the file ABseeD002.txt.$ 
$ 
$ cat ABseeD002.txt
049050051052053
054051052053

If you don't want to see the end junk, then you need to look at how you copy a fragment of a string, and how you take care of the \0 at the end of the string.

[cprogramnoob]

I charge for looking at your answer. ;-)

[cprogramnoob]

COMMANDS TO EMPTY A STRING

memset(message_cache1,0,sizeof(message_cache1));  --> SUCCESSS

strcpy(message_cache1, "");  --> FAIL (LEFT gibberish hidden)

[hamster_nz]

COMMANDS TO EMPTY A STRING

memset(message_cache1,0,sizeof(message_cache1));  --> SUCCESSS

strcpy(message_cache1, "");  --> FAIL (LEFT gibberish hidden)

The string is only valid up to and including the terminating null character, so the second one is not a fail.

[Salem]

lengthofcache1:1
21	        if ((strlen(message_cache1)) > 5) { 
(gdb) n
27	        printf("\n%s\n", message_cache1);
(gdb) 

6
28	        printf("\n%s\n", message_cache2);
(gdb) 


29	        for  (int count=0; count <=4; count++) // review for loops maybe sing a song about them.
(gdb) 
31	                int ascii_cache=message_cache1[count];
(gdb) p message_cache1
$5 = "6\000\063\064\065\066", '\000' <repeats 233 times>

Your for loop blindly assumes there are 5 characters in the buffer.

Any loop dealing with strings needs to check for the \0 character.

[cprogramnoob]

Thank you for helping be careful of the gibberish against me out there. When I say FAIL it failed for me. Your success was not mine.