Java jjwt creating invalid JSON for JWT

I must be missing something. I am using the JJWT library to create JWTs. The JWTs are created inconsistently from the library depending on the data set in the claims. My code:

Date now = new Date();
Date expiration = new Date(now.getTime() + TimeUnit.MINUTES.toMillis(30));

Claims claims = Jwts.claims();

JSONObject jsonObject = new JSONObject();
jsonObject.put("serviceName1", "serviceStatus1");
jsonObject.put("serviceName2", "serviceStatus2");
claims.put("services",jsonObject);

claims.setSubject("225544");
claims.setExpiration(expiration);
claims.setId(UUID.randomUUID().toString());
claims.setIssuedAt(now);

return Jwts.builder()
    .setClaims(claims)
    .signWith(SignatureAlgorithm.HS256, Base64.encodeBase64(secret.getBytes()))
    .compact();

This code creates a JWT and signs it correctly. However, when the payload is decoded, the payload value is not always valid JSON. Most often it is missing the closing } causing any parsing of it to fail. If the Subject is 8 characters, it works fine. If it is 7 or 6 characters long, it is invalid JSON. Or if I add other tags to the claim, sometimes it works and sometimes it doesn't. Am I doing something wrong?

I have also tried using Auth0 java-JWT library and get similar results, Payload not always valid JSON.

Ultimately, I could not get the JJWT library working how I wanted. As such, I implemented a simple hashing algorithm and jwt creator manually. Here is what that looks like:

    Date now = new Date();
    //Valid only for 30 minutes
    Date expiration = new Date(now.getTime() + TimeUnit.MINUTES.toMillis(30));

    JSONObject header = new JSONObject();
    JSONObject payload = new JSONObject();

    header.put("alg", "HS256");

    payload.put("sub", "ourSubject");
    payload.put("exp", expiration.getTime() / 1000);
    payload.put("jti", UUID.randomUUID().toString());
    payload.put("iat", now.getTime() / 1000);
    payload.put("services", "JSON object of our custom data needed in authorization (not authentication");
    String signature = "";

    StringBuilder token = new StringBuilder();
    token.append(new String(Base64.encodeBase64(header.toString().getBytes())));
    token.append(".");
    token.append(new String(Base64.encodeBase64(payload.toString().getBytes())));
    try {
        Mac sha256_HMAC = Mac.getInstance("HmacSHA256");
        SecretKeySpec secret_key = new SecretKeySpec(Base64.encodeBase64((secret + otherPartOfSecret).getBytes()), "HmacSHA256");
        sha256_HMAC.init(secret_key);

        signature = new String(Base64.encodeBase64(sha256_HMAC.doFinal(token.toString().getBytes())));
    } catch (Exception e) {
        System.out.println("Error");
    }

    token.append(".");
    token.append(signature);

    return token.toString();