PrometheusDuplicateTimestamps errors with log_to_metrics filter starting in fluent-bit 3.1.5

## Bug Report

**Describe the bug**
After upgrading from fluent-bit 3.1.4 to 3.1.5 all our k8s clusters start reporting PrometheusDuplicateTimestamps errors
Prometheus metric `rate(prometheus_target_scrapes_sample_duplicate_timestamp_total}[5m]) > 0` is increasing.
Prometheus is logging a lot of warnings like this:
```
ts=2024-09-23T16:22:32.820Z caller=scrape.go:1754 level=warn component="scrape manager" scrape_pool=serviceMonitor/platform-logging/fluent-bit/1 target=http://10.67.3.197:2021/metrics msg="Error on ingesting samples with different value but same timestamp" num_dropped=32
ts=2024-09-23T16:22:38.237Z caller=scrape.go:1754 level=warn component="scrape manager" scrape_pool=serviceMonitor/platform-logging/fluent-bit/1 target=http://10.67.4.81:2021/metrics msg="Error on ingesting samples with different value but same timestamp" num_dropped=1876
ts=2024-09-23T16:22:39.697Z caller=scrape.go:1754 level=warn component="scrape manager" scrape_pool=serviceMonitor/platform-logging/fluent-bit/1 target=http://10.67.13.208:2021/metrics msg="Error on ingesting samples with different value but same timestamp" num_dropped=4
ts=2024-09-23T16:22:41.643Z caller=scrape.go:1754 level=warn component="scrape manager" scrape_pool=serviceMonitor/platform-logging/fluent-bit/1 target=http://10.67.3.110:2021/metrics msg="Error on ingesting samples with different value but same timestamp" num_dropped=7
```

**To Reproduce**
- Steps to reproduce the problem:
- Deploy fluent-bit with the below tail input config as a daemonset into a k8s cluster using version 3.1.4 to see container logs and metrics to validate success.
- Update fluent-bit image to 3.1.5 (or newer, <= 3.1.8) and verify `/metrics` endpoint on port 2021

**Expected behavior**
No duplicate metrics on the additional endpoint `/metrics` for log_to_metrics feature usually on port 2021, no warnings in Prometheus logs, no PrometheusDuplicateTimestamps errors.

**Screenshots**

**Your Environment**

* Version used: 3.1.5 (or higher) tested until 3.1.8, issue is still present.
* Configuration: (Helm chart values)
```
serviceMonitor:
enabled: true
interval: 10s
scrapeTimeout: 10s
additionalEndpoints:
- port: log-metrics
path: /metrics
interval: 10s
scrapeTimeout: 10s

extraPorts:
- port: 2021
containerPort: 2021
protocol: TCP
name: log-metrics

config:
service: |
[SERVICE]
Flush 1
Daemon Off
Log_Level info
Parsers_File parsers.conf
Parsers_File custom_parsers.conf
HTTP_Server On
HTTP_Listen 0.0.0.0
HTTP_Port {{ .Values.service.port }}

inputs: |
[INPUT]
Name tail
Tag kube.*
Alias tail_container_logs
Path /var/log/containers/*.log
multiline.parser docker, cri
DB /var/log/flb_kube.db
DB.locking true
Mem_Buf_Limit 32MB
Skip_Long_Lines On

filters: |
[FILTER]
Name kubernetes
Alias kubernetes_all
Match kube.*
Merge_Log On
Keep_Log Off
K8S-Logging.Parser On
K8S-Logging.Exclude On
Annotations Off
Buffer_Size 1MB
Use_Kubelet true

[FILTER]
name log_to_metrics
match kube.*
tag log_counter_metric
metric_mode counter
metric_name kubernetes_messages
metric_description This metric counts Kubernetes messages
kubernetes_mode true

outputs: |
[OUTPUT]
name prometheus_exporter
match log_counter_metric
host 0.0.0.0
port 2021

```
* Environment name and version (e.g. Kubernetes? What version?):
* EKS; Kubernetes 1.30
* Server type and version:
* Operating System and version:
* EKS on Bottlerocket OS 1.22.0 (aws-k8s-1.30) Kernel version 6.1.106 containerd://1.7.20+bottlerocket
* Filters and plugins:
* kubernetes, log_to_metrics

**Additional context**
It is just very annoying when every k8s cluster with this common configuration reports PrometheusDuplicateTimestamps errors